Starting phenix.real_space_refine on Sun Sep 29 12:12:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhj_14733/09_2024/7zhj_14733.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhj_14733/09_2024/7zhj_14733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhj_14733/09_2024/7zhj_14733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhj_14733/09_2024/7zhj_14733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhj_14733/09_2024/7zhj_14733.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zhj_14733/09_2024/7zhj_14733.cif" } resolution = 3.53 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 46908 2.51 5 N 12429 2.21 5 O 14829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74346 Number of models: 1 Model: "" Number of chains: 33 Chain: "R" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "I" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "a" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Q" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "S" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "F" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "N" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "H" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "X" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Y" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "M" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "O" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "E" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "C" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "J" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "L" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "G" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "W" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "U" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "K" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "D" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "A" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "B" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "P" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "T" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "f" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 262 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "g" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 262 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "e" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 262 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "V" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Z" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "b" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7577 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Chain: "d" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7577 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Chain: "c" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7577 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 36, 'TRANS': 912} Time building chain proxies: 33.29, per 1000 atoms: 0.45 Number of scatterers: 74346 At special positions: 0 Unit cell: (170.226, 183.736, 333.697, 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 180 16.00 O 14829 8.00 N 12429 7.00 C 46908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS b 316 " - pdb=" SG CYS b 327 " distance=2.03 Simple disulfide: pdb=" SG CYS d 316 " - pdb=" SG CYS d 327 " distance=2.03 Simple disulfide: pdb=" SG CYS c 316 " - pdb=" SG CYS c 327 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.59 Conformation dependent library (CDL) restraints added in 7.1 seconds 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17742 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 136 sheets defined 14.1% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.98 Creating SS restraints... Processing helix chain 'R' and resid 3 through 7 removed outlier: 3.972A pdb=" N VAL R 7 " --> pdb=" O GLU R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 92 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 76 through 83 Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.596A pdb=" N ILE I 204 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 16 Processing helix chain 'a' and resid 58 through 76 Processing helix chain 'a' and resid 83 through 87 Processing helix chain 'Q' and resid 81 through 91 Processing helix chain 'S' and resid 81 through 92 removed outlier: 3.653A pdb=" N LYS S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 7 No H-bonds generated for 'chain 'F' and resid 5 through 7' Processing helix chain 'F' and resid 91 through 100 Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 192 through 201 Processing helix chain 'F' and resid 275 through 287 removed outlier: 3.522A pdb=" N LEU F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 removed outlier: 4.254A pdb=" N GLY F 346 " --> pdb=" O LEU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'N' and resid 3 through 7 removed outlier: 3.974A pdb=" N VAL N 7 " --> pdb=" O GLU N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 92 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.595A pdb=" N ILE H 204 " --> pdb=" O ILE H 201 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 76 Processing helix chain 'Y' and resid 12 through 16 Processing helix chain 'Y' and resid 58 through 76 Processing helix chain 'Y' and resid 83 through 87 Processing helix chain 'M' and resid 81 through 91 Processing helix chain 'O' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS O 91 " --> pdb=" O THR O 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 7 No H-bonds generated for 'chain 'E' and resid 5 through 7' Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.520A pdb=" N LEU E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 346 removed outlier: 4.256A pdb=" N GLY E 346 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.685A pdb=" N TRP C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'J' and resid 3 through 7 removed outlier: 3.972A pdb=" N VAL J 7 " --> pdb=" O GLU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 92 Processing helix chain 'L' and resid 81 through 91 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 76 through 83 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.595A pdb=" N ILE G 204 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 16 Processing helix chain 'W' and resid 58 through 76 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'U' and resid 81 through 91 Processing helix chain 'K' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.521A pdb=" N LEU D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 removed outlier: 4.255A pdb=" N GLY D 346 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.687A pdb=" N TRP A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'B' and resid 91 through 100 removed outlier: 3.684A pdb=" N TRP B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'P' and resid 81 through 91 Processing helix chain 'T' and resid 81 through 91 Processing helix chain 'f' and resid 1186 through 1193 removed outlier: 3.901A pdb=" N PHE f1190 " --> pdb=" O SER f1186 " (cutoff:3.500A) Processing helix chain 'f' and resid 1194 through 1207 removed outlier: 3.720A pdb=" N ALA f1205 " --> pdb=" O ALA f1201 " (cutoff:3.500A) Processing helix chain 'f' and resid 1212 through 1216 removed outlier: 3.646A pdb=" N SER f1215 " --> pdb=" O THR f1212 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU f1216 " --> pdb=" O LEU f1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 1212 through 1216' Processing helix chain 'g' and resid 1186 through 1193 removed outlier: 3.902A pdb=" N PHE g1190 " --> pdb=" O SER g1186 " (cutoff:3.500A) Processing helix chain 'g' and resid 1194 through 1207 removed outlier: 3.719A pdb=" N ALA g1205 " --> pdb=" O ALA g1201 " (cutoff:3.500A) Processing helix chain 'g' and resid 1212 through 1216 removed outlier: 3.647A pdb=" N SER g1215 " --> pdb=" O THR g1212 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU g1216 " --> pdb=" O LEU g1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 1212 through 1216' Processing helix chain 'e' and resid 1186 through 1193 removed outlier: 3.902A pdb=" N PHE e1190 " --> pdb=" O SER e1186 " (cutoff:3.500A) Processing helix chain 'e' and resid 1194 through 1207 removed outlier: 3.719A pdb=" N ALA e1205 " --> pdb=" O ALA e1201 " (cutoff:3.500A) Processing helix chain 'e' and resid 1212 through 1216 removed outlier: 3.645A pdb=" N SER e1215 " --> pdb=" O THR e1212 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU e1216 " --> pdb=" O LEU e1213 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1212 through 1216' Processing helix chain 'V' and resid 58 through 76 Processing helix chain 'Z' and resid 58 through 76 Processing helix chain 'b' and resid 5 through 15 removed outlier: 3.656A pdb=" N ASN b 13 " --> pdb=" O LYS b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 94 removed outlier: 3.988A pdb=" N LYS b 91 " --> pdb=" O ASP b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 174 through 179 Processing helix chain 'b' and resid 196 through 202 removed outlier: 3.671A pdb=" N GLN b 200 " --> pdb=" O PRO b 197 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU b 201 " --> pdb=" O GLU b 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 217 removed outlier: 4.664A pdb=" N THR b 212 " --> pdb=" O SER b 208 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR b 213 " --> pdb=" O ASN b 209 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS b 217 " --> pdb=" O THR b 213 " (cutoff:3.500A) Processing helix chain 'b' and resid 241 through 249 removed outlier: 3.607A pdb=" N VAL b 249 " --> pdb=" O TYR b 245 " (cutoff:3.500A) Processing helix chain 'b' and resid 258 through 263 removed outlier: 3.630A pdb=" N LYS b 262 " --> pdb=" O LEU b 259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE b 263 " --> pdb=" O ALA b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 318 through 323 removed outlier: 3.543A pdb=" N ASP b 323 " --> pdb=" O GLU b 319 " (cutoff:3.500A) Processing helix chain 'b' and resid 339 through 344 Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.611A pdb=" N LYS b 389 " --> pdb=" O ASP b 385 " (cutoff:3.500A) Processing helix chain 'b' and resid 392 through 398 Processing helix chain 'b' and resid 401 through 405 removed outlier: 3.531A pdb=" N TRP b 405 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing helix chain 'b' and resid 459 through 469 Processing helix chain 'b' and resid 478 through 482 removed outlier: 3.553A pdb=" N PHE b 482 " --> pdb=" O LEU b 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 483 through 495 removed outlier: 3.695A pdb=" N ILE b 493 " --> pdb=" O SER b 489 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU b 494 " --> pdb=" O GLU b 490 " (cutoff:3.500A) Processing helix chain 'b' and resid 502 through 506 Processing helix chain 'b' and resid 509 through 513 removed outlier: 3.532A pdb=" N VAL b 512 " --> pdb=" O TRP b 509 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY b 513 " --> pdb=" O ARG b 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 509 through 513' Processing helix chain 'b' and resid 536 through 545 Processing helix chain 'b' and resid 576 through 578 No H-bonds generated for 'chain 'b' and resid 576 through 578' Processing helix chain 'b' and resid 616 through 622 Processing helix chain 'b' and resid 623 through 626 Processing helix chain 'b' and resid 639 through 655 removed outlier: 3.759A pdb=" N ARG b 655 " --> pdb=" O LEU b 651 " (cutoff:3.500A) Processing helix chain 'b' and resid 713 through 717 Processing helix chain 'b' and resid 870 through 874 removed outlier: 3.985A pdb=" N GLU b 874 " --> pdb=" O PRO b 871 " (cutoff:3.500A) Processing helix chain 'b' and resid 907 through 921 removed outlier: 3.539A pdb=" N ASN b 911 " --> pdb=" O LEU b 907 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE b 915 " --> pdb=" O ASN b 911 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA b 916 " --> pdb=" O LYS b 912 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN b 919 " --> pdb=" O PHE b 915 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 15 removed outlier: 3.656A pdb=" N ASN d 13 " --> pdb=" O LYS d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 94 removed outlier: 3.989A pdb=" N LYS d 91 " --> pdb=" O ASP d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 179 Processing helix chain 'd' and resid 196 through 202 removed outlier: 3.670A pdb=" N GLN d 200 " --> pdb=" O PRO d 197 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU d 201 " --> pdb=" O GLU d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 207 through 217 removed outlier: 4.663A pdb=" N THR d 212 " --> pdb=" O SER d 208 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR d 213 " --> pdb=" O ASN d 209 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS d 217 " --> pdb=" O THR d 213 " (cutoff:3.500A) Processing helix chain 'd' and resid 241 through 249 removed outlier: 3.607A pdb=" N VAL d 249 " --> pdb=" O TYR d 245 " (cutoff:3.500A) Processing helix chain 'd' and resid 258 through 263 removed outlier: 3.631A pdb=" N LYS d 262 " --> pdb=" O LEU d 259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE d 263 " --> pdb=" O ALA d 260 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 323 removed outlier: 3.542A pdb=" N ASP d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) Processing helix chain 'd' and resid 339 through 344 Processing helix chain 'd' and resid 380 through 389 removed outlier: 3.611A pdb=" N LYS d 389 " --> pdb=" O ASP d 385 " (cutoff:3.500A) Processing helix chain 'd' and resid 392 through 398 Processing helix chain 'd' and resid 401 through 405 removed outlier: 3.531A pdb=" N TRP d 405 " --> pdb=" O PRO d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 469 Processing helix chain 'd' and resid 478 through 482 removed outlier: 3.552A pdb=" N PHE d 482 " --> pdb=" O LEU d 479 " (cutoff:3.500A) Processing helix chain 'd' and resid 483 through 495 removed outlier: 3.695A pdb=" N ILE d 493 " --> pdb=" O SER d 489 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU d 494 " --> pdb=" O GLU d 490 " (cutoff:3.500A) Processing helix chain 'd' and resid 502 through 506 Processing helix chain 'd' and resid 509 through 513 removed outlier: 3.533A pdb=" N VAL d 512 " --> pdb=" O TRP d 509 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY d 513 " --> pdb=" O ARG d 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 509 through 513' Processing helix chain 'd' and resid 536 through 545 Processing helix chain 'd' and resid 576 through 578 No H-bonds generated for 'chain 'd' and resid 576 through 578' Processing helix chain 'd' and resid 616 through 622 Processing helix chain 'd' and resid 623 through 626 Processing helix chain 'd' and resid 639 through 655 removed outlier: 3.759A pdb=" N ARG d 655 " --> pdb=" O LEU d 651 " (cutoff:3.500A) Processing helix chain 'd' and resid 713 through 717 Processing helix chain 'd' and resid 870 through 874 removed outlier: 3.984A pdb=" N GLU d 874 " --> pdb=" O PRO d 871 " (cutoff:3.500A) Processing helix chain 'd' and resid 907 through 921 removed outlier: 3.539A pdb=" N ASN d 911 " --> pdb=" O LEU d 907 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE d 915 " --> pdb=" O ASN d 911 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA d 916 " --> pdb=" O LYS d 912 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN d 919 " --> pdb=" O PHE d 915 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 15 removed outlier: 3.655A pdb=" N ASN c 13 " --> pdb=" O LYS c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 94 removed outlier: 3.988A pdb=" N LYS c 91 " --> pdb=" O ASP c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 179 Processing helix chain 'c' and resid 196 through 202 removed outlier: 3.671A pdb=" N GLN c 200 " --> pdb=" O PRO c 197 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU c 201 " --> pdb=" O GLU c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 217 removed outlier: 4.664A pdb=" N THR c 212 " --> pdb=" O SER c 208 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR c 213 " --> pdb=" O ASN c 209 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS c 217 " --> pdb=" O THR c 213 " (cutoff:3.500A) Processing helix chain 'c' and resid 241 through 249 removed outlier: 3.608A pdb=" N VAL c 249 " --> pdb=" O TYR c 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 258 through 263 removed outlier: 3.631A pdb=" N LYS c 262 " --> pdb=" O LEU c 259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE c 263 " --> pdb=" O ALA c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 318 through 323 removed outlier: 3.543A pdb=" N ASP c 323 " --> pdb=" O GLU c 319 " (cutoff:3.500A) Processing helix chain 'c' and resid 339 through 344 Processing helix chain 'c' and resid 380 through 389 removed outlier: 3.611A pdb=" N LYS c 389 " --> pdb=" O ASP c 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 392 through 398 Processing helix chain 'c' and resid 401 through 405 removed outlier: 3.531A pdb=" N TRP c 405 " --> pdb=" O PRO c 402 " (cutoff:3.500A) Processing helix chain 'c' and resid 459 through 469 Processing helix chain 'c' and resid 478 through 482 removed outlier: 3.552A pdb=" N PHE c 482 " --> pdb=" O LEU c 479 " (cutoff:3.500A) Processing helix chain 'c' and resid 483 through 495 removed outlier: 3.695A pdb=" N ILE c 493 " --> pdb=" O SER c 489 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU c 494 " --> pdb=" O GLU c 490 " (cutoff:3.500A) Processing helix chain 'c' and resid 502 through 506 Processing helix chain 'c' and resid 509 through 513 removed outlier: 3.531A pdb=" N VAL c 512 " --> pdb=" O TRP c 509 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY c 513 " --> pdb=" O ARG c 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 509 through 513' Processing helix chain 'c' and resid 536 through 545 Processing helix chain 'c' and resid 576 through 578 No H-bonds generated for 'chain 'c' and resid 576 through 578' Processing helix chain 'c' and resid 616 through 622 Processing helix chain 'c' and resid 623 through 626 Processing helix chain 'c' and resid 639 through 655 removed outlier: 3.759A pdb=" N ARG c 655 " --> pdb=" O LEU c 651 " (cutoff:3.500A) Processing helix chain 'c' and resid 713 through 717 Processing helix chain 'c' and resid 870 through 874 removed outlier: 3.984A pdb=" N GLU c 874 " --> pdb=" O PRO c 871 " (cutoff:3.500A) Processing helix chain 'c' and resid 907 through 921 removed outlier: 3.539A pdb=" N ASN c 911 " --> pdb=" O LEU c 907 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE c 915 " --> pdb=" O ASN c 911 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA c 916 " --> pdb=" O LYS c 912 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN c 919 " --> pdb=" O PHE c 915 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.339A pdb=" N LEU R 10 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER R 135 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL R 12 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL R 111 " --> pdb=" O ILE R 127 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU R 129 " --> pdb=" O TYR R 109 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR R 109 " --> pdb=" O GLU R 129 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS R 131 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY R 107 " --> pdb=" O LYS R 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR R 133 " --> pdb=" O LEU R 105 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU R 105 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER R 135 " --> pdb=" O GLN R 103 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN R 103 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP R 110 " --> pdb=" O SER R 49 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE R 50 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.785A pdb=" N LEU R 80 " --> pdb=" O TYR R 18 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL R 75 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER R 77 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE R 68 " --> pdb=" O SER R 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.577A pdb=" N LYS H 230 " --> pdb=" O PHE I 2 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 15 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 18 through 21 current: chain 'I' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 62 through 68 current: chain 'I' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 90 through 92 current: chain 'I' and resid 115 through 131 removed outlier: 6.411A pdb=" N GLY I 141 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL I 127 " --> pdb=" O ASN I 139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN I 139 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE I 129 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE I 137 " --> pdb=" O PHE I 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 137 through 143 current: chain 'I' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 177 through 178 current: chain 'I' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 213 through 227 current: chain 'I' and resid 255 through 269 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 275 through 282 current: chain 'G' and resid 52 through 59 Processing sheet with id=AA6, first strand: chain 'I' and resid 31 through 39 removed outlier: 4.643A pdb=" N SER I 33 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA I 57 " --> pdb=" O GLN I 35 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE I 37 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE I 55 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR I 39 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER I 53 " --> pdb=" O THR I 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 52 through 59 current: chain 'H' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 21 current: chain 'H' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 62 through 68 current: chain 'H' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 90 through 92 current: chain 'H' and resid 115 through 131 removed outlier: 6.409A pdb=" N GLY H 141 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL H 127 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN H 139 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE H 129 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE H 137 " --> pdb=" O PHE H 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 137 through 143 current: chain 'H' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 177 through 178 current: chain 'H' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 213 through 227 current: chain 'H' and resid 255 through 269 Processing sheet with id=AA7, first strand: chain 'a' and resid 79 through 81 removed outlier: 5.239A pdb=" N TRP a 48 " --> pdb=" O GLU a 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN a 25 " --> pdb=" O TYR a 47 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER a 19 " --> pdb=" O SER a 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL a 20 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR Z 186 " --> pdb=" O SER Z 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER Z 194 " --> pdb=" O THR Z 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 38 through 42 current: chain 'V' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 38 through 41 current: chain 'b' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 659 through 664 current: chain 'b' and resid 689 through 698 removed outlier: 6.451A pdb=" N VAL b 707 " --> pdb=" O ASP b 694 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL b 696 " --> pdb=" O ASN b 705 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN b 705 " --> pdb=" O VAL b 696 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 704 through 710 current: chain 'd' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 38 through 42 current: chain 'd' and resid 77 through 81 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 77 through 81 current: chain 'd' and resid 128 through 135 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 128 through 135 current: chain 'd' and resid 149 through 159 Processing sheet with id=AA9, first strand: chain 'a' and resid 92 through 93 Processing sheet with id=AB1, first strand: chain 'a' and resid 108 through 112 removed outlier: 7.156A pdb=" N VAL a 147 " --> pdb=" O SER a 143 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER a 143 " --> pdb=" O VAL a 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN a 149 " --> pdb=" O PHE a 141 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE a 141 " --> pdb=" O ASN a 149 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER a 151 " --> pdb=" O THR a 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 182 through 183 current: chain 'a' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 193 through 194 current: chain 'V' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 47 through 53 current: chain 'V' and resid 173 through 177 Processing sheet with id=AB3, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.529A pdb=" N LEU Q 10 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER Q 135 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL Q 12 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG Q 126 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE Q 113 " --> pdb=" O ARG Q 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET Q 128 " --> pdb=" O VAL Q 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY Q 130 " --> pdb=" O TYR Q 109 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE Q 134 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU Q 105 " --> pdb=" O ILE Q 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA Q 62 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 18 through 23 removed outlier: 7.473A pdb=" N VAL Q 75 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL Q 69 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 25 through 28 removed outlier: 3.814A pdb=" N THR Q 35 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU S 10 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER S 135 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL S 12 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL S 111 " --> pdb=" O ILE S 127 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU S 129 " --> pdb=" O TYR S 109 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR S 109 " --> pdb=" O GLU S 129 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS S 131 " --> pdb=" O GLY S 107 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY S 107 " --> pdb=" O LYS S 131 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR S 133 " --> pdb=" O LEU S 105 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU S 105 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER S 135 " --> pdb=" O GLN S 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN S 103 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP S 110 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER S 49 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.751A pdb=" N TYR S 18 " --> pdb=" O LEU S 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 26 through 28 removed outlier: 3.730A pdb=" N LYS S 37 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP S 28 " --> pdb=" O THR S 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE F 11 " --> pdb=" O ILE F 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 28 current: chain 'F' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 75 current: chain 'F' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 119 through 122 current: chain 'F' and resid 143 through 159 removed outlier: 5.644A pdb=" N ILE F 152 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN F 172 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN F 158 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ARG F 166 " --> pdb=" O ASN F 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 166 through 173 current: chain 'F' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 221 through 222 current: chain 'F' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 260 through 268 current: chain 'F' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 309 through 319 current: chain 'F' and resid 331 through 338 Processing sheet with id=AC1, first strand: chain 'F' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER F 64 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR F 43 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN F 62 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 79 through 80 Processing sheet with id=AC3, first strand: chain 'F' and resid 238 through 239 Processing sheet with id=AC4, first strand: chain 'F' and resid 378 through 382 removed outlier: 3.558A pdb=" N ALA F 378 " --> pdb=" O THR F 403 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR F 380 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F 401 " --> pdb=" O THR F 380 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 389 through 390 removed outlier: 3.917A pdb=" N LEU F 390 " --> pdb=" O THR F 459 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL F 440 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AC7, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.339A pdb=" N LEU N 10 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER N 135 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL N 12 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL N 111 " --> pdb=" O ILE N 127 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU N 129 " --> pdb=" O TYR N 109 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR N 109 " --> pdb=" O GLU N 129 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS N 131 " --> pdb=" O GLY N 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY N 107 " --> pdb=" O LYS N 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR N 133 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU N 105 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER N 135 " --> pdb=" O GLN N 103 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN N 103 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP N 110 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE N 50 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.785A pdb=" N LEU N 80 " --> pdb=" O TYR N 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL N 75 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER N 77 " --> pdb=" O ILE N 68 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE N 68 " --> pdb=" O SER N 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AD1, first strand: chain 'H' and resid 31 through 39 removed outlier: 4.643A pdb=" N SER H 33 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 57 " --> pdb=" O GLN H 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE H 37 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE H 55 " --> pdb=" O PHE H 37 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR H 39 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N SER H 53 " --> pdb=" O THR H 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 52 through 59 current: chain 'G' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 21 current: chain 'G' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 62 through 68 current: chain 'G' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 92 current: chain 'G' and resid 115 through 131 removed outlier: 6.407A pdb=" N GLY G 141 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL G 127 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN G 139 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE G 129 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE G 137 " --> pdb=" O PHE G 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 137 through 143 current: chain 'G' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 177 through 178 current: chain 'G' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 213 through 227 current: chain 'G' and resid 255 through 269 Processing sheet with id=AD2, first strand: chain 'X' and resid 19 through 25 removed outlier: 3.530A pdb=" N ASN X 25 " --> pdb=" O TYR X 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 47 through 53 current: chain 'X' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 197 through 202 current: chain 'W' and resid 193 through 194 Processing sheet with id=AD3, first strand: chain 'X' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 38 through 41 current: chain 'W' and resid 38 through 42 removed outlier: 8.701A pdb=" N LEU b 18 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU W 40 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR b 20 " --> pdb=" O GLU W 40 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS W 42 " --> pdb=" O THR b 20 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N CYS b 22 " --> pdb=" O LYS W 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 38 through 42 current: chain 'b' and resid 77 through 81 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 77 through 81 current: chain 'b' and resid 128 through 135 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 128 through 135 current: chain 'b' and resid 149 through 159 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 149 through 159 current: chain 'c' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 659 through 664 current: chain 'c' and resid 689 through 698 removed outlier: 6.451A pdb=" N VAL c 707 " --> pdb=" O ASP c 694 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL c 696 " --> pdb=" O ASN c 705 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN c 705 " --> pdb=" O VAL c 696 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 108 through 112 removed outlier: 6.965A pdb=" N VAL X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER X 143 " --> pdb=" O VAL X 147 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN X 149 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE X 141 " --> pdb=" O ASN X 149 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER X 151 " --> pdb=" O THR X 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS X 128 " --> pdb=" O VAL X 167 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 193 through 194 removed outlier: 3.506A pdb=" N SER X 194 " --> pdb=" O THR X 186 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR X 186 " --> pdb=" O SER X 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL Y 20 " --> pdb=" O LEU X 187 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER Y 19 " --> pdb=" O SER Y 53 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN Y 25 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP Y 48 " --> pdb=" O GLU Y 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 42 current: chain 'Z' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 38 through 41 current: chain 'd' and resid 659 through 664 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 659 through 664 current: chain 'd' and resid 689 through 698 removed outlier: 6.451A pdb=" N VAL d 707 " --> pdb=" O ASP d 694 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL d 696 " --> pdb=" O ASN d 705 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN d 705 " --> pdb=" O VAL d 696 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 704 through 710 current: chain 'c' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 38 through 42 current: chain 'c' and resid 77 through 81 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 77 through 81 current: chain 'c' and resid 128 through 135 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 128 through 135 current: chain 'c' and resid 149 through 159 Processing sheet with id=AD7, first strand: chain 'Y' and resid 92 through 93 Processing sheet with id=AD8, first strand: chain 'Y' and resid 108 through 112 removed outlier: 7.157A pdb=" N VAL Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N SER Y 143 " --> pdb=" O VAL Y 147 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN Y 149 " --> pdb=" O PHE Y 141 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE Y 141 " --> pdb=" O ASN Y 149 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER Y 151 " --> pdb=" O THR Y 139 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 182 through 183 current: chain 'Y' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 193 through 194 current: chain 'Z' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 47 through 53 current: chain 'Z' and resid 173 through 177 Processing sheet with id=AE1, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU M 10 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER M 135 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL M 12 " --> pdb=" O SER M 135 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG M 126 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE M 113 " --> pdb=" O ARG M 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET M 128 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY M 130 " --> pdb=" O TYR M 109 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE M 134 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU M 105 " --> pdb=" O ILE M 134 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA M 62 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 18 through 23 removed outlier: 7.473A pdb=" N VAL M 75 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL M 69 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 25 through 28 removed outlier: 3.813A pdb=" N THR M 35 " --> pdb=" O ASP M 28 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU O 10 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER O 135 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL O 12 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL O 111 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU O 129 " --> pdb=" O TYR O 109 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR O 109 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS O 131 " --> pdb=" O GLY O 107 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY O 107 " --> pdb=" O LYS O 131 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR O 133 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU O 105 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER O 135 " --> pdb=" O GLN O 103 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN O 103 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP O 110 " --> pdb=" O SER O 49 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER O 49 " --> pdb=" O ASP O 110 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 18 through 23 removed outlier: 3.751A pdb=" N TYR O 18 " --> pdb=" O LEU O 80 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 26 through 28 removed outlier: 3.732A pdb=" N LYS O 37 " --> pdb=" O ASP O 26 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP O 28 " --> pdb=" O THR O 35 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE E 11 " --> pdb=" O ILE E 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 28 current: chain 'E' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 75 current: chain 'E' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 119 through 122 current: chain 'E' and resid 143 through 159 removed outlier: 5.644A pdb=" N ILE E 152 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN E 172 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN E 158 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG E 166 " --> pdb=" O ASN E 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 166 through 173 current: chain 'E' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 221 through 222 current: chain 'E' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 268 current: chain 'E' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 309 through 319 current: chain 'E' and resid 331 through 338 Processing sheet with id=AE8, first strand: chain 'E' and resid 40 through 44 removed outlier: 3.917A pdb=" N SER E 64 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR E 43 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN E 62 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 79 through 80 Processing sheet with id=AF1, first strand: chain 'E' and resid 238 through 239 Processing sheet with id=AF2, first strand: chain 'E' and resid 378 through 382 removed outlier: 3.557A pdb=" N ALA E 378 " --> pdb=" O THR E 403 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR E 380 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU E 401 " --> pdb=" O THR E 380 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 389 through 390 removed outlier: 3.915A pdb=" N LEU E 390 " --> pdb=" O THR E 459 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 440 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 396 through 397 Processing sheet with id=AF5, first strand: chain 'C' and resid 9 through 14 removed outlier: 3.582A pdb=" N VAL C 13 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN C 26 " --> pdb=" O VAL C 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 75 current: chain 'C' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 119 through 122 current: chain 'C' and resid 143 through 160 removed outlier: 5.715A pdb=" N ILE C 152 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN C 172 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG C 166 " --> pdb=" O ASN C 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 173 current: chain 'C' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 268 current: chain 'C' and resid 307 through 319 Processing sheet with id=AF6, first strand: chain 'C' and resid 40 through 46 removed outlier: 6.772A pdb=" N ASN C 41 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AF8, first strand: chain 'C' and resid 237 through 239 removed outlier: 4.149A pdb=" N THR C 238 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 378 through 382 removed outlier: 3.893A pdb=" N ALA C 378 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 380 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 401 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.912A pdb=" N LEU C 390 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 456 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 442 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 440 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 395 through 397 Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.338A pdb=" N LEU J 10 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER J 135 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL J 12 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL J 111 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU J 129 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR J 109 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS J 131 " --> pdb=" O GLY J 107 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY J 107 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR J 133 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU J 105 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER J 135 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN J 103 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP J 110 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE J 50 " --> pdb=" O VAL J 61 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.784A pdb=" N LEU J 80 " --> pdb=" O TYR J 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL J 75 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER J 77 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE J 68 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 25 through 27 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.503A pdb=" N LEU L 10 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER L 135 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL L 12 " --> pdb=" O SER L 135 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER L 124 " --> pdb=" O ARG L 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG L 115 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG L 126 " --> pdb=" O ILE L 113 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE L 113 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET L 128 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL L 111 " --> pdb=" O MET L 128 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE L 134 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU L 105 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 49 " --> pdb=" O ASP L 110 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE L 44 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE L 68 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU L 46 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR L 66 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY L 48 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA L 62 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR L 66 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER L 79 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE L 68 " --> pdb=" O SER L 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER L 77 " --> pdb=" O ILE L 68 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AG8, first strand: chain 'W' and resid 79 through 81 removed outlier: 5.238A pdb=" N TRP W 48 " --> pdb=" O GLU W 202 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN W 25 " --> pdb=" O TYR W 47 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER W 19 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL W 20 " --> pdb=" O LEU V 187 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR V 186 " --> pdb=" O SER V 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER V 194 " --> pdb=" O THR V 186 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 92 through 93 Processing sheet with id=AH1, first strand: chain 'W' and resid 108 through 112 removed outlier: 7.156A pdb=" N VAL W 147 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER W 143 " --> pdb=" O VAL W 147 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN W 149 " --> pdb=" O PHE W 141 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE W 141 " --> pdb=" O ASN W 149 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER W 151 " --> pdb=" O THR W 139 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU U 10 " --> pdb=" O TYR U 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER U 135 " --> pdb=" O LEU U 10 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL U 12 " --> pdb=" O SER U 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG U 126 " --> pdb=" O ILE U 113 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE U 113 " --> pdb=" O ARG U 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET U 128 " --> pdb=" O VAL U 111 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY U 130 " --> pdb=" O TYR U 109 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE U 134 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU U 105 " --> pdb=" O ILE U 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA U 62 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 18 through 23 removed outlier: 7.474A pdb=" N VAL U 75 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL U 69 " --> pdb=" O VAL U 75 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.813A pdb=" N THR U 35 " --> pdb=" O ASP U 28 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.415A pdb=" N LEU K 10 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER K 135 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL K 12 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL K 111 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU K 129 " --> pdb=" O TYR K 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR K 109 " --> pdb=" O GLU K 129 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS K 131 " --> pdb=" O GLY K 107 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY K 107 " --> pdb=" O LYS K 131 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR K 133 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU K 105 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER K 135 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN K 103 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP K 110 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER K 49 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.750A pdb=" N TYR K 18 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.732A pdb=" N LYS K 37 " --> pdb=" O ASP K 26 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP K 28 " --> pdb=" O THR K 35 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 9 through 14 removed outlier: 4.240A pdb=" N ILE D 11 " --> pdb=" O ILE D 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 28 current: chain 'D' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 75 current: chain 'D' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 119 through 122 current: chain 'D' and resid 143 through 159 removed outlier: 5.642A pdb=" N ILE D 152 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN D 172 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN D 158 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG D 166 " --> pdb=" O ASN D 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 166 through 173 current: chain 'D' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 221 through 222 current: chain 'D' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 260 through 268 current: chain 'D' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 309 through 319 current: chain 'D' and resid 331 through 338 Processing sheet with id=AH9, first strand: chain 'D' and resid 40 through 44 removed outlier: 3.917A pdb=" N SER D 64 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR D 43 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN D 62 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 79 through 80 Processing sheet with id=AI2, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AI3, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.557A pdb=" N ALA D 378 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 380 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 401 " --> pdb=" O THR D 380 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.916A pdb=" N LEU D 390 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 440 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AI6, first strand: chain 'A' and resid 9 through 14 removed outlier: 3.582A pdb=" N VAL A 13 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 26 " --> pdb=" O VAL A 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 75 current: chain 'A' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 122 current: chain 'A' and resid 143 through 160 removed outlier: 5.714A pdb=" N ILE A 152 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 172 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG A 166 " --> pdb=" O ASN A 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 268 current: chain 'A' and resid 307 through 319 Processing sheet with id=AI7, first strand: chain 'A' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AI9, first strand: chain 'A' and resid 237 through 239 removed outlier: 4.150A pdb=" N THR A 238 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'A' and resid 378 through 382 removed outlier: 3.892A pdb=" N ALA A 378 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 380 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 401 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.912A pdb=" N LEU A 390 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 456 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 442 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 440 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'A' and resid 395 through 397 Processing sheet with id=AJ4, first strand: chain 'B' and resid 9 through 14 removed outlier: 3.583A pdb=" N VAL B 13 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 26 " --> pdb=" O VAL B 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 75 current: chain 'B' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 119 through 122 current: chain 'B' and resid 143 through 160 removed outlier: 5.715A pdb=" N ILE B 152 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN B 172 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG B 166 " --> pdb=" O ASN B 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 173 current: chain 'B' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 260 through 268 current: chain 'B' and resid 307 through 319 Processing sheet with id=AJ5, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN B 41 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AJ7, first strand: chain 'B' and resid 237 through 239 removed outlier: 4.150A pdb=" N THR B 238 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.893A pdb=" N ALA B 378 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 380 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 401 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.913A pdb=" N LEU B 390 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 456 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 442 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 440 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'B' and resid 395 through 397 Processing sheet with id=AK2, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.503A pdb=" N LEU P 10 " --> pdb=" O TYR P 133 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER P 135 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL P 12 " --> pdb=" O SER P 135 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER P 124 " --> pdb=" O ARG P 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG P 115 " --> pdb=" O SER P 124 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG P 126 " --> pdb=" O ILE P 113 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE P 113 " --> pdb=" O ARG P 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET P 128 " --> pdb=" O VAL P 111 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL P 111 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE P 134 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU P 105 " --> pdb=" O ILE P 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER P 49 " --> pdb=" O ASP P 110 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE P 44 " --> pdb=" O ILE P 68 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE P 68 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU P 46 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR P 66 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY P 48 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA P 62 " --> pdb=" O ILE P 50 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR P 66 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER P 79 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE P 68 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER P 77 " --> pdb=" O ILE P 68 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'P' and resid 25 through 26 Processing sheet with id=AK4, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.504A pdb=" N LEU T 10 " --> pdb=" O TYR T 133 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER T 135 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL T 12 " --> pdb=" O SER T 135 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER T 124 " --> pdb=" O ARG T 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG T 115 " --> pdb=" O SER T 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG T 126 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE T 113 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET T 128 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL T 111 " --> pdb=" O MET T 128 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE T 134 " --> pdb=" O LEU T 105 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU T 105 " --> pdb=" O ILE T 134 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER T 49 " --> pdb=" O ASP T 110 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE T 44 " --> pdb=" O ILE T 68 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE T 68 " --> pdb=" O PHE T 44 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU T 46 " --> pdb=" O THR T 66 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR T 66 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY T 48 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA T 62 " --> pdb=" O ILE T 50 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR T 66 " --> pdb=" O SER T 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER T 79 " --> pdb=" O THR T 66 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE T 68 " --> pdb=" O SER T 77 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER T 77 " --> pdb=" O ILE T 68 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'T' and resid 25 through 26 Processing sheet with id=AK6, first strand: chain 'V' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER V 143 " --> pdb=" O VAL V 147 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN V 149 " --> pdb=" O PHE V 141 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE V 141 " --> pdb=" O ASN V 149 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER V 151 " --> pdb=" O THR V 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS V 128 " --> pdb=" O VAL V 167 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'Z' and resid 108 through 112 removed outlier: 6.965A pdb=" N VAL Z 147 " --> pdb=" O SER Z 143 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER Z 143 " --> pdb=" O VAL Z 147 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN Z 149 " --> pdb=" O PHE Z 141 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE Z 141 " --> pdb=" O ASN Z 149 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER Z 151 " --> pdb=" O THR Z 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Z 128 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'b' and resid 48 through 50 Processing sheet with id=AK9, first strand: chain 'b' and resid 181 through 183 Processing sheet with id=AL1, first strand: chain 'b' and resid 227 through 228 Processing sheet with id=AL2, first strand: chain 'b' and resid 304 through 308 removed outlier: 8.119A pdb=" N PHE b 304 " --> pdb=" O GLN b 438 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN b 438 " --> pdb=" O PHE b 304 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP b 306 " --> pdb=" O GLU b 436 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY b 439 " --> pdb=" O GLY b 269 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY b 269 " --> pdb=" O GLY b 439 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'b' and resid 276 through 282 removed outlier: 6.059A pdb=" N ALA b 295 " --> pdb=" O PRO b 277 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE b 279 " --> pdb=" O VAL b 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 289 through 295 current: chain 'b' and resid 365 through 367 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 365 through 367 current: chain 'b' and resid 416 through 422 Processing sheet with id=AL4, first strand: chain 'b' and resid 444 through 445 Processing sheet with id=AL5, first strand: chain 'b' and resid 551 through 553 removed outlier: 3.620A pdb=" N THR b 562 " --> pdb=" O ALA b 551 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'b' and resid 609 through 615 removed outlier: 3.519A pdb=" N VAL b 596 " --> pdb=" O PHE b 614 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER b 595 " --> pdb=" O LEU b 630 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'b' and resid 740 through 745 removed outlier: 4.431A pdb=" N PHE b 742 " --> pdb=" O SER b 762 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER b 762 " --> pdb=" O PHE b 742 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR b 744 " --> pdb=" O GLU b 760 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU b 760 " --> pdb=" O TYR b 744 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY b 759 " --> pdb=" O ILE b 802 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'b' and resid 785 through 788 removed outlier: 7.082A pdb=" N VAL b 817 " --> pdb=" O VAL b 772 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'b' and resid 808 through 814 removed outlier: 3.630A pdb=" N ALA b 810 " --> pdb=" O VAL b 831 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'b' and resid 843 through 848 removed outlier: 6.006A pdb=" N ASN b 844 " --> pdb=" O ASP b 868 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP b 868 " --> pdb=" O ASN b 844 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS b 864 " --> pdb=" O VAL b 848 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL b 863 " --> pdb=" O TYR b 906 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'b' and resid 892 through 898 Processing sheet with id=AM3, first strand: chain 'd' and resid 48 through 50 Processing sheet with id=AM4, first strand: chain 'd' and resid 181 through 183 Processing sheet with id=AM5, first strand: chain 'd' and resid 227 through 228 Processing sheet with id=AM6, first strand: chain 'd' and resid 304 through 308 removed outlier: 8.119A pdb=" N PHE d 304 " --> pdb=" O GLN d 438 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN d 438 " --> pdb=" O PHE d 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP d 306 " --> pdb=" O GLU d 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY d 439 " --> pdb=" O GLY d 269 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY d 269 " --> pdb=" O GLY d 439 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'd' and resid 276 through 282 removed outlier: 6.058A pdb=" N ALA d 295 " --> pdb=" O PRO d 277 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE d 279 " --> pdb=" O VAL d 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 289 through 295 current: chain 'd' and resid 365 through 367 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 365 through 367 current: chain 'd' and resid 416 through 422 Processing sheet with id=AM8, first strand: chain 'd' and resid 444 through 445 Processing sheet with id=AM9, first strand: chain 'd' and resid 551 through 553 removed outlier: 3.619A pdb=" N THR d 562 " --> pdb=" O ALA d 551 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'd' and resid 609 through 615 removed outlier: 3.519A pdb=" N VAL d 596 " --> pdb=" O PHE d 614 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER d 595 " --> pdb=" O LEU d 630 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'd' and resid 740 through 745 removed outlier: 4.432A pdb=" N PHE d 742 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER d 762 " --> pdb=" O PHE d 742 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR d 744 " --> pdb=" O GLU d 760 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU d 760 " --> pdb=" O TYR d 744 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY d 759 " --> pdb=" O ILE d 802 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'd' and resid 785 through 788 removed outlier: 7.082A pdb=" N VAL d 817 " --> pdb=" O VAL d 772 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'd' and resid 808 through 814 removed outlier: 3.631A pdb=" N ALA d 810 " --> pdb=" O VAL d 831 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'd' and resid 843 through 848 removed outlier: 6.005A pdb=" N ASN d 844 " --> pdb=" O ASP d 868 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP d 868 " --> pdb=" O ASN d 844 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS d 864 " --> pdb=" O VAL d 848 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL d 863 " --> pdb=" O TYR d 906 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'd' and resid 892 through 898 Processing sheet with id=AN7, first strand: chain 'c' and resid 48 through 50 Processing sheet with id=AN8, first strand: chain 'c' and resid 181 through 183 Processing sheet with id=AN9, first strand: chain 'c' and resid 227 through 228 Processing sheet with id=AO1, first strand: chain 'c' and resid 304 through 308 removed outlier: 8.118A pdb=" N PHE c 304 " --> pdb=" O GLN c 438 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN c 438 " --> pdb=" O PHE c 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP c 306 " --> pdb=" O GLU c 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY c 439 " --> pdb=" O GLY c 269 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY c 269 " --> pdb=" O GLY c 439 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'c' and resid 276 through 282 removed outlier: 6.059A pdb=" N ALA c 295 " --> pdb=" O PRO c 277 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE c 279 " --> pdb=" O VAL c 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 289 through 295 current: chain 'c' and resid 365 through 367 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 365 through 367 current: chain 'c' and resid 416 through 422 Processing sheet with id=AO3, first strand: chain 'c' and resid 444 through 445 Processing sheet with id=AO4, first strand: chain 'c' and resid 551 through 553 removed outlier: 3.620A pdb=" N THR c 562 " --> pdb=" O ALA c 551 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'c' and resid 609 through 615 removed outlier: 3.519A pdb=" N VAL c 596 " --> pdb=" O PHE c 614 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER c 595 " --> pdb=" O LEU c 630 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'c' and resid 740 through 745 removed outlier: 4.431A pdb=" N PHE c 742 " --> pdb=" O SER c 762 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER c 762 " --> pdb=" O PHE c 742 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR c 744 " --> pdb=" O GLU c 760 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU c 760 " --> pdb=" O TYR c 744 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY c 759 " --> pdb=" O ILE c 802 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'c' and resid 785 through 788 removed outlier: 7.082A pdb=" N VAL c 817 " --> pdb=" O VAL c 772 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'c' and resid 808 through 814 removed outlier: 3.631A pdb=" N ALA c 810 " --> pdb=" O VAL c 831 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'c' and resid 843 through 848 removed outlier: 6.006A pdb=" N ASN c 844 " --> pdb=" O ASP c 868 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP c 868 " --> pdb=" O ASN c 844 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS c 864 " --> pdb=" O VAL c 848 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL c 863 " --> pdb=" O TYR c 906 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'c' and resid 892 through 898 1472 hydrogen bonds defined for protein. 3858 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: 30.84 Time building geometry restraints manager: 16.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23937 1.34 - 1.46: 12093 1.46 - 1.58: 39411 1.58 - 1.69: 0 1.69 - 1.81: 333 Bond restraints: 75774 Sorted by residual: bond pdb=" N VAL Z 41 " pdb=" CA VAL Z 41 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.20e-02 6.94e+03 8.34e+00 bond pdb=" N VAL X 41 " pdb=" CA VAL X 41 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.17e+00 bond pdb=" N ILE d 898 " pdb=" CA ILE d 898 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.05e+00 bond pdb=" N THR L 66 " pdb=" CA THR L 66 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.94e+00 bond pdb=" N ILE c 898 " pdb=" CA ILE c 898 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 7.92e+00 ... (remaining 75769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 101090 1.73 - 3.46: 1700 3.46 - 5.19: 131 5.19 - 6.92: 10 6.92 - 8.65: 11 Bond angle restraints: 102942 Sorted by residual: angle pdb=" CA PRO P 33 " pdb=" N PRO P 33 " pdb=" CD PRO P 33 " ideal model delta sigma weight residual 112.00 105.06 6.94 1.40e+00 5.10e-01 2.46e+01 angle pdb=" CA PRO T 33 " pdb=" N PRO T 33 " pdb=" CD PRO T 33 " ideal model delta sigma weight residual 112.00 105.08 6.92 1.40e+00 5.10e-01 2.44e+01 angle pdb=" CA PRO L 33 " pdb=" N PRO L 33 " pdb=" CD PRO L 33 " ideal model delta sigma weight residual 112.00 105.10 6.90 1.40e+00 5.10e-01 2.43e+01 angle pdb=" CA GLY d 924 " pdb=" C GLY d 924 " pdb=" O GLY d 924 " ideal model delta sigma weight residual 121.62 118.14 3.48 9.80e-01 1.04e+00 1.26e+01 angle pdb=" CA GLY b 924 " pdb=" C GLY b 924 " pdb=" O GLY b 924 " ideal model delta sigma weight residual 121.62 118.15 3.47 9.80e-01 1.04e+00 1.25e+01 ... (remaining 102937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 41736 17.80 - 35.60: 3076 35.60 - 53.40: 515 53.40 - 71.20: 81 71.20 - 88.99: 54 Dihedral angle restraints: 45462 sinusoidal: 17781 harmonic: 27681 Sorted by residual: dihedral pdb=" CB CYS b 316 " pdb=" SG CYS b 316 " pdb=" SG CYS b 327 " pdb=" CB CYS b 327 " ideal model delta sinusoidal sigma weight residual 93.00 43.98 49.02 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS c 316 " pdb=" SG CYS c 316 " pdb=" SG CYS c 327 " pdb=" CB CYS c 327 " ideal model delta sinusoidal sigma weight residual 93.00 43.98 49.02 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS d 316 " pdb=" SG CYS d 316 " pdb=" SG CYS d 327 " pdb=" CB CYS d 327 " ideal model delta sinusoidal sigma weight residual 93.00 44.01 48.99 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 45459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 8110 0.039 - 0.077: 2361 0.077 - 0.116: 1085 0.116 - 0.154: 185 0.154 - 0.193: 31 Chirality restraints: 11772 Sorted by residual: chirality pdb=" CA ILE L 78 " pdb=" N ILE L 78 " pdb=" C ILE L 78 " pdb=" CB ILE L 78 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ILE P 78 " pdb=" N ILE P 78 " pdb=" C ILE P 78 " pdb=" CB ILE P 78 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA ILE T 78 " pdb=" N ILE T 78 " pdb=" C ILE T 78 " pdb=" CB ILE T 78 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 11769 not shown) Planarity restraints: 13344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 32 " 0.076 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO L 33 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO L 33 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO L 33 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR P 32 " -0.076 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO P 33 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO P 33 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO P 33 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR T 32 " -0.076 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO T 33 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO T 33 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO T 33 " -0.060 5.00e-02 4.00e+02 ... (remaining 13341 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 2163 2.70 - 3.25: 73625 3.25 - 3.80: 113852 3.80 - 4.35: 156057 4.35 - 4.90: 261872 Nonbonded interactions: 607569 Sorted by model distance: nonbonded pdb=" OD1 ASP Z 31 " pdb=" CE LYS c 61 " model vdw 2.151 3.440 nonbonded pdb=" OD1 ASP F 163 " pdb=" N ILE F 164 " model vdw 2.156 3.120 nonbonded pdb=" OD1 ASP D 163 " pdb=" N ILE D 164 " model vdw 2.156 3.120 nonbonded pdb=" OD1 ASP E 163 " pdb=" N ILE E 164 " model vdw 2.158 3.120 nonbonded pdb=" O HIS d 372 " pdb=" NE2 GLN d 377 " model vdw 2.216 3.120 ... (remaining 607564 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 2 through 140) selection = (chain 'M' and resid 2 through 140) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 2 through 140) selection = (chain 'Q' and resid 2 through 140) selection = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 2 through 140) selection = (chain 'U' and resid 2 through 140) } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'e' selection = chain 'f' selection = chain 'g' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 2.300 Check model and map are aligned: 0.440 Set scattering table: 0.540 Process input model: 133.410 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.003 0.077 75774 Z= 0.212 Angle : 0.548 8.646 102942 Z= 0.321 Chirality : 0.045 0.193 11772 Planarity : 0.004 0.111 13344 Dihedral : 13.017 88.994 27711 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.71 (0.08), residues: 9462 helix: -0.35 (0.16), residues: 1050 sheet: -1.00 (0.09), residues: 3462 loop : -1.35 (0.08), residues: 4950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 369 HIS 0.008 0.001 HIS b 339 PHE 0.014 0.001 PHE H 92 TYR 0.022 0.001 TYR B 239 ARG 0.009 0.000 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2243 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2240 time to evaluate : 7.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 22 MET cc_start: 0.6127 (mtp) cc_final: 0.5905 (mtp) REVERT: R 36 SER cc_start: 0.6726 (m) cc_final: 0.6443 (p) REVERT: R 41 LEU cc_start: 0.7108 (mt) cc_final: 0.6743 (tp) REVERT: R 56 ASP cc_start: 0.6201 (p0) cc_final: 0.5827 (p0) REVERT: R 97 ASP cc_start: 0.6739 (t70) cc_final: 0.6171 (t0) REVERT: R 131 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7706 (mttp) REVERT: I 16 ASP cc_start: 0.7800 (t0) cc_final: 0.7286 (t0) REVERT: I 27 ASN cc_start: 0.8286 (t0) cc_final: 0.7923 (t0) REVERT: I 62 SER cc_start: 0.8369 (m) cc_final: 0.8088 (p) REVERT: I 143 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7462 (mm-30) REVERT: I 187 MET cc_start: 0.8140 (mpp) cc_final: 0.7921 (mpp) REVERT: I 244 THR cc_start: 0.8443 (p) cc_final: 0.8228 (m) REVERT: a 24 ASP cc_start: 0.7936 (t0) cc_final: 0.7450 (t70) REVERT: a 155 ASP cc_start: 0.6663 (m-30) cc_final: 0.6439 (m-30) REVERT: Q 6 ARG cc_start: 0.5948 (mmt90) cc_final: 0.4567 (ptp90) REVERT: Q 139 THR cc_start: 0.7878 (t) cc_final: 0.7276 (m) REVERT: Q 140 GLN cc_start: 0.6476 (tp-100) cc_final: 0.5855 (tp40) REVERT: F 141 ASP cc_start: 0.5703 (m-30) cc_final: 0.5207 (m-30) REVERT: N 41 LEU cc_start: 0.7738 (mt) cc_final: 0.7296 (tp) REVERT: N 100 ASN cc_start: 0.5860 (t0) cc_final: 0.5508 (m-40) REVERT: H 27 ASN cc_start: 0.8180 (t0) cc_final: 0.7819 (t0) REVERT: H 62 SER cc_start: 0.8427 (m) cc_final: 0.8128 (p) REVERT: H 237 PHE cc_start: 0.7945 (t80) cc_final: 0.7543 (t80) REVERT: X 105 LYS cc_start: 0.8142 (ptpp) cc_final: 0.7892 (pttp) REVERT: X 186 THR cc_start: 0.7922 (m) cc_final: 0.7567 (t) REVERT: Y 24 ASP cc_start: 0.8194 (t0) cc_final: 0.7699 (t70) REVERT: M 6 ARG cc_start: 0.5899 (mmt90) cc_final: 0.4558 (ptt90) REVERT: M 139 THR cc_start: 0.7470 (t) cc_final: 0.7168 (m) REVERT: O 14 GLU cc_start: 0.6541 (tt0) cc_final: 0.6299 (tt0) REVERT: O 97 ASP cc_start: 0.7600 (t0) cc_final: 0.7166 (t0) REVERT: O 136 ASP cc_start: 0.8013 (m-30) cc_final: 0.7750 (m-30) REVERT: E 2 SER cc_start: 0.6877 (p) cc_final: 0.6425 (m) REVERT: E 142 LYS cc_start: 0.7525 (mmtt) cc_final: 0.7238 (ptmm) REVERT: E 209 THR cc_start: 0.6927 (m) cc_final: 0.6656 (m) REVERT: E 239 TYR cc_start: 0.7673 (m-80) cc_final: 0.7446 (m-80) REVERT: E 283 LEU cc_start: 0.8789 (mm) cc_final: 0.8512 (mt) REVERT: E 379 ILE cc_start: 0.6871 (mt) cc_final: 0.6391 (pt) REVERT: C 11 ILE cc_start: 0.6240 (mm) cc_final: 0.5434 (tp) REVERT: C 23 THR cc_start: 0.5291 (p) cc_final: 0.5004 (p) REVERT: C 79 TYR cc_start: 0.4766 (p90) cc_final: 0.4467 (p90) REVERT: C 126 ASN cc_start: 0.7052 (p0) cc_final: 0.6701 (p0) REVERT: C 139 LEU cc_start: 0.3669 (tp) cc_final: 0.1880 (tp) REVERT: C 153 ASN cc_start: 0.6019 (t0) cc_final: 0.5698 (t0) REVERT: C 197 MET cc_start: 0.5694 (mmp) cc_final: 0.5391 (mmt) REVERT: C 213 ILE cc_start: 0.6162 (tp) cc_final: 0.5959 (tp) REVERT: C 220 LYS cc_start: 0.7592 (mtpt) cc_final: 0.6924 (ptpp) REVERT: C 233 ILE cc_start: 0.6894 (mp) cc_final: 0.6329 (tt) REVERT: C 281 LYS cc_start: 0.7029 (pttt) cc_final: 0.6097 (tttm) REVERT: C 404 PRO cc_start: 0.1637 (Cg_endo) cc_final: 0.1259 (Cg_exo) REVERT: C 411 GLU cc_start: 0.5890 (mm-30) cc_final: 0.5689 (pt0) REVERT: C 442 VAL cc_start: 0.5790 (p) cc_final: 0.5306 (p) REVERT: J 22 MET cc_start: 0.5898 (mtp) cc_final: 0.5274 (mmm) REVERT: J 26 ASP cc_start: 0.4928 (p0) cc_final: 0.3505 (t0) REVERT: J 56 ASP cc_start: 0.6264 (p0) cc_final: 0.6022 (m-30) REVERT: J 131 LYS cc_start: 0.8622 (mtmt) cc_final: 0.7811 (mttp) REVERT: L 16 VAL cc_start: 0.6789 (t) cc_final: 0.6586 (t) REVERT: L 42 THR cc_start: 0.8031 (m) cc_final: 0.7513 (t) REVERT: L 108 TYR cc_start: 0.7831 (m-80) cc_final: 0.7562 (m-80) REVERT: L 115 ARG cc_start: 0.5535 (ttp-170) cc_final: 0.4371 (ptt180) REVERT: L 135 SER cc_start: 0.8621 (t) cc_final: 0.8178 (p) REVERT: G 16 ASP cc_start: 0.7585 (t0) cc_final: 0.7300 (t0) REVERT: G 27 ASN cc_start: 0.8096 (t0) cc_final: 0.7636 (t0) REVERT: G 35 GLN cc_start: 0.8147 (mt0) cc_final: 0.7754 (tt0) REVERT: G 62 SER cc_start: 0.8277 (m) cc_final: 0.7860 (p) REVERT: G 104 MET cc_start: 0.8641 (mmt) cc_final: 0.8379 (mmm) REVERT: G 244 THR cc_start: 0.8063 (p) cc_final: 0.7802 (m) REVERT: W 86 TYR cc_start: 0.8323 (m-80) cc_final: 0.8078 (m-80) REVERT: W 125 ASP cc_start: 0.6943 (m-30) cc_final: 0.6679 (t70) REVERT: W 202 GLU cc_start: 0.8103 (tt0) cc_final: 0.7889 (tt0) REVERT: W 204 LEU cc_start: 0.8122 (pp) cc_final: 0.7726 (pp) REVERT: U 6 ARG cc_start: 0.5950 (mmt90) cc_final: 0.4542 (ptp90) REVERT: U 115 ARG cc_start: 0.6384 (ptm-80) cc_final: 0.5910 (tmm-80) REVERT: U 138 VAL cc_start: 0.7935 (m) cc_final: 0.7703 (m) REVERT: U 139 THR cc_start: 0.7408 (t) cc_final: 0.6904 (m) REVERT: U 140 GLN cc_start: 0.6984 (tp-100) cc_final: 0.6573 (tp40) REVERT: K 28 ASP cc_start: 0.5190 (t70) cc_final: 0.4961 (t0) REVERT: D 26 GLN cc_start: 0.6741 (pm20) cc_final: 0.6498 (pm20) REVERT: D 286 THR cc_start: 0.7497 (p) cc_final: 0.7224 (p) REVERT: D 292 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7268 (ttt180) REVERT: D 379 ILE cc_start: 0.6907 (mt) cc_final: 0.6413 (pt) REVERT: D 392 ARG cc_start: 0.5822 (mtm180) cc_final: 0.5401 (ttm110) REVERT: A 152 ILE cc_start: 0.5311 (mm) cc_final: 0.5110 (mm) REVERT: A 220 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7324 (ptpp) REVERT: A 222 TYR cc_start: 0.4579 (m-80) cc_final: 0.4215 (m-80) REVERT: A 233 ILE cc_start: 0.7339 (mp) cc_final: 0.6840 (tt) REVERT: A 281 LYS cc_start: 0.6628 (pttt) cc_final: 0.5883 (tttp) REVERT: A 286 THR cc_start: 0.4394 (m) cc_final: 0.4056 (m) REVERT: A 318 HIS cc_start: 0.5116 (t-90) cc_final: 0.4882 (t-90) REVERT: A 339 ILE cc_start: 0.6935 (pt) cc_final: 0.6597 (mt) REVERT: A 348 GLU cc_start: 0.5641 (mm-30) cc_final: 0.5143 (mp0) REVERT: A 404 PRO cc_start: 0.2570 (Cg_endo) cc_final: 0.2266 (Cg_exo) REVERT: A 408 ARG cc_start: 0.5999 (mmm-85) cc_final: 0.5433 (tpp80) REVERT: B 126 ASN cc_start: 0.6799 (p0) cc_final: 0.6470 (p0) REVERT: B 220 LYS cc_start: 0.7146 (mtpt) cc_final: 0.6750 (ttpp) REVERT: B 281 LYS cc_start: 0.7137 (pttt) cc_final: 0.6138 (tttp) REVERT: B 339 ILE cc_start: 0.7221 (pt) cc_final: 0.6772 (mt) REVERT: B 390 LEU cc_start: 0.5992 (tp) cc_final: 0.5543 (mt) REVERT: B 401 GLU cc_start: 0.3187 (pp20) cc_final: 0.2916 (pp20) REVERT: B 408 ARG cc_start: 0.5991 (mmm-85) cc_final: 0.5601 (tpp80) REVERT: P 9 ASP cc_start: 0.8053 (m-30) cc_final: 0.7463 (m-30) REVERT: P 35 THR cc_start: 0.6707 (p) cc_final: 0.6462 (p) REVERT: P 42 THR cc_start: 0.7938 (m) cc_final: 0.6937 (p) REVERT: P 44 PHE cc_start: 0.7322 (m-10) cc_final: 0.6743 (m-80) REVERT: P 56 ASP cc_start: 0.6674 (p0) cc_final: 0.6473 (p0) REVERT: P 70 ASP cc_start: 0.7200 (t70) cc_final: 0.6788 (t70) REVERT: P 112 ILE cc_start: 0.8200 (mt) cc_final: 0.7992 (mt) REVERT: P 115 ARG cc_start: 0.6344 (ttp-170) cc_final: 0.4645 (ptt180) REVERT: T 9 ASP cc_start: 0.7985 (m-30) cc_final: 0.7760 (m-30) REVERT: T 42 THR cc_start: 0.8019 (m) cc_final: 0.7060 (p) REVERT: T 44 PHE cc_start: 0.7128 (m-10) cc_final: 0.6377 (m-80) REVERT: T 70 ASP cc_start: 0.7302 (t70) cc_final: 0.6837 (t70) REVERT: T 115 ARG cc_start: 0.6146 (ttp-170) cc_final: 0.5118 (ptt180) REVERT: T 135 SER cc_start: 0.8654 (t) cc_final: 0.8052 (p) REVERT: f 1204 LEU cc_start: 0.8730 (tp) cc_final: 0.8435 (tp) REVERT: e 1193 ASN cc_start: 0.7436 (m110) cc_final: 0.6788 (m110) REVERT: V 68 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7701 (mmm160) REVERT: V 70 LEU cc_start: 0.8332 (mt) cc_final: 0.8011 (mp) REVERT: V 105 LYS cc_start: 0.7985 (ptpp) cc_final: 0.7556 (pttp) REVERT: V 110 ILE cc_start: 0.7950 (mt) cc_final: 0.7738 (mm) REVERT: V 175 THR cc_start: 0.7819 (p) cc_final: 0.7542 (p) REVERT: Z 105 LYS cc_start: 0.7885 (ptpp) cc_final: 0.7493 (pttp) REVERT: b 28 LEU cc_start: 0.7818 (mp) cc_final: 0.7588 (mp) REVERT: b 95 ASN cc_start: 0.7956 (m-40) cc_final: 0.7702 (m-40) REVERT: b 141 LYS cc_start: 0.7785 (ttmm) cc_final: 0.7459 (tttm) REVERT: b 252 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7190 (mt-10) REVERT: b 368 ILE cc_start: 0.8023 (mm) cc_final: 0.7819 (mm) REVERT: b 886 TYR cc_start: 0.6699 (m-80) cc_final: 0.5738 (m-10) REVERT: b 918 LEU cc_start: 0.7605 (pp) cc_final: 0.7148 (mm) REVERT: d 300 GLU cc_start: 0.7374 (tt0) cc_final: 0.7131 (tt0) REVERT: d 858 PHE cc_start: 0.4427 (m-10) cc_final: 0.4138 (p90) REVERT: d 886 TYR cc_start: 0.7121 (m-80) cc_final: 0.6894 (m-10) REVERT: c 11 TYR cc_start: 0.8403 (t80) cc_final: 0.7902 (t80) REVERT: c 252 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7056 (tt0) REVERT: c 368 ILE cc_start: 0.8003 (mm) cc_final: 0.7769 (mm) REVERT: c 918 LEU cc_start: 0.7448 (pp) cc_final: 0.6958 (mm) REVERT: c 926 ASN cc_start: 0.5561 (m-40) cc_final: 0.5001 (t0) outliers start: 3 outliers final: 2 residues processed: 2240 average time/residue: 0.7095 time to fit residues: 2703.9515 Evaluate side-chains 1228 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1226 time to evaluate : 6.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 863 VAL Chi-restraints excluded: chain c residue 863 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 790 optimal weight: 5.9990 chunk 709 optimal weight: 6.9990 chunk 393 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 chunk 478 optimal weight: 10.0000 chunk 379 optimal weight: 4.9990 chunk 733 optimal weight: 5.9990 chunk 283 optimal weight: 6.9990 chunk 446 optimal weight: 2.9990 chunk 546 optimal weight: 7.9990 chunk 849 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 45 HIS I 161 GLN I 216 ASN S 15 ASN S 103 GLN S 140 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN F 151 GLN H 35 GLN H 210 ASN H 216 ASN O 103 GLN E 151 GLN E 172 ASN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 113 HIS ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 ASN L 100 ASN G 112 HIS G 216 ASN K 103 GLN D 172 ASN A 20 HIS A 41 ASN A 66 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS B 26 GLN B 66 ASN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 154 GLN B 158 ASN T 15 ASN g1193 ASN b 178 HIS ** b 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 521 ASN ** b 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 734 ASN d 178 HIS ** d 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 594 ASN d 734 ASN c 178 HIS ** c 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 506 GLN ** c 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 594 ASN c 911 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 75774 Z= 0.513 Angle : 0.764 12.099 102942 Z= 0.405 Chirality : 0.053 0.362 11772 Planarity : 0.006 0.071 13344 Dihedral : 5.601 78.523 10370 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.07 % Allowed : 11.60 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -2.02 (0.08), residues: 9462 helix: -0.83 (0.15), residues: 1128 sheet: -1.12 (0.09), residues: 3159 loop : -1.58 (0.08), residues: 5175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 70 HIS 0.013 0.003 HIS B 113 PHE 0.027 0.003 PHE I 78 TYR 0.032 0.003 TYR b 681 ARG 0.016 0.001 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1218 time to evaluate : 6.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 LEU cc_start: 0.7532 (mt) cc_final: 0.7290 (tp) REVERT: R 56 ASP cc_start: 0.6293 (p0) cc_final: 0.5997 (m-30) REVERT: R 131 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8168 (mttp) REVERT: I 1 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6732 (mtm) REVERT: I 296 GLU cc_start: 0.7272 (tp30) cc_final: 0.6547 (pt0) REVERT: a 155 ASP cc_start: 0.7601 (m-30) cc_final: 0.7348 (m-30) REVERT: Q 6 ARG cc_start: 0.6170 (mmt90) cc_final: 0.4313 (ptp90) REVERT: S 10 LEU cc_start: 0.8343 (mt) cc_final: 0.8001 (mp) REVERT: S 131 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8229 (mtmm) REVERT: F 5 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8349 (mp) REVERT: F 224 ILE cc_start: 0.8962 (mm) cc_final: 0.8699 (mm) REVERT: F 382 LYS cc_start: 0.5633 (ttmt) cc_final: 0.5095 (mmtm) REVERT: N 46 LEU cc_start: 0.8085 (pt) cc_final: 0.7792 (pp) REVERT: N 73 GLN cc_start: 0.7020 (tp40) cc_final: 0.6708 (tp40) REVERT: N 86 THR cc_start: 0.8543 (p) cc_final: 0.8102 (p) REVERT: H 35 GLN cc_start: 0.8122 (mt0) cc_final: 0.7918 (mt0) REVERT: H 62 SER cc_start: 0.8507 (m) cc_final: 0.8241 (p) REVERT: H 137 ILE cc_start: 0.8894 (tt) cc_final: 0.8635 (pt) REVERT: H 237 PHE cc_start: 0.8005 (t80) cc_final: 0.7652 (t80) REVERT: X 70 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8334 (mp) REVERT: Y 71 GLU cc_start: 0.8225 (tp30) cc_final: 0.8003 (tp30) REVERT: M 6 ARG cc_start: 0.6341 (mmt90) cc_final: 0.4684 (ptt90) REVERT: M 140 GLN cc_start: 0.7139 (tp-100) cc_final: 0.6788 (tp40) REVERT: O 105 LEU cc_start: 0.8549 (tp) cc_final: 0.8336 (tp) REVERT: O 128 MET cc_start: 0.7907 (ptp) cc_final: 0.7694 (ptp) REVERT: O 131 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8312 (mtmt) REVERT: E 151 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8507 (mm-40) REVERT: E 170 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7741 (p) REVERT: E 344 ASP cc_start: 0.6701 (p0) cc_final: 0.6248 (t0) REVERT: E 362 ILE cc_start: 0.8851 (pt) cc_final: 0.8483 (mt) REVERT: C 4 GLN cc_start: 0.5227 (mm-40) cc_final: 0.4160 (tp40) REVERT: C 79 TYR cc_start: 0.4957 (p90) cc_final: 0.4200 (p90) REVERT: C 93 MET cc_start: 0.5838 (mtt) cc_final: 0.5292 (mtp) REVERT: C 126 ASN cc_start: 0.7254 (p0) cc_final: 0.7020 (p0) REVERT: C 197 MET cc_start: 0.6045 (mmp) cc_final: 0.5749 (mmt) REVERT: C 216 MET cc_start: 0.5738 (mmm) cc_final: 0.5464 (mmt) REVERT: C 224 ILE cc_start: 0.6061 (mm) cc_final: 0.5799 (mt) REVERT: C 281 LYS cc_start: 0.7339 (pttt) cc_final: 0.6152 (ttmm) REVERT: C 293 PHE cc_start: 0.6174 (m-80) cc_final: 0.5959 (m-80) REVERT: C 297 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7842 (mt) REVERT: J 22 MET cc_start: 0.5888 (mtp) cc_final: 0.4970 (mmm) REVERT: J 26 ASP cc_start: 0.4127 (p0) cc_final: 0.3248 (t70) REVERT: J 56 ASP cc_start: 0.6777 (p0) cc_final: 0.6467 (m-30) REVERT: J 113 ILE cc_start: 0.8615 (tt) cc_final: 0.8409 (tt) REVERT: J 131 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7974 (mttp) REVERT: L 37 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7141 (ptmt) REVERT: L 42 THR cc_start: 0.8309 (m) cc_final: 0.7841 (p) REVERT: L 60 THR cc_start: 0.8726 (m) cc_final: 0.8515 (t) REVERT: L 100 ASN cc_start: 0.7852 (t0) cc_final: 0.7555 (t0) REVERT: L 115 ARG cc_start: 0.6055 (ttp-170) cc_final: 0.5097 (ptt180) REVERT: G 16 ASP cc_start: 0.7737 (t0) cc_final: 0.7439 (t0) REVERT: G 27 ASN cc_start: 0.8491 (t0) cc_final: 0.8231 (t0) REVERT: G 35 GLN cc_start: 0.8455 (mt0) cc_final: 0.7967 (tt0) REVERT: G 62 SER cc_start: 0.8351 (m) cc_final: 0.7909 (p) REVERT: G 101 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: G 192 GLN cc_start: 0.7602 (tp40) cc_final: 0.7313 (tp40) REVERT: W 125 ASP cc_start: 0.7643 (m-30) cc_final: 0.7228 (m-30) REVERT: U 6 ARG cc_start: 0.5790 (mmt90) cc_final: 0.4396 (ptp90) REVERT: U 115 ARG cc_start: 0.6785 (ptm-80) cc_final: 0.6337 (tmm-80) REVERT: K 8 ILE cc_start: 0.8426 (tt) cc_final: 0.8219 (tp) REVERT: K 131 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8107 (mtmm) REVERT: D 74 THR cc_start: 0.8575 (p) cc_final: 0.8353 (t) REVERT: D 170 SER cc_start: 0.8100 (t) cc_final: 0.7703 (p) REVERT: D 260 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6702 (mp0) REVERT: D 362 ILE cc_start: 0.8743 (pt) cc_final: 0.8442 (mt) REVERT: A 64 SER cc_start: 0.8107 (t) cc_final: 0.7893 (p) REVERT: A 126 ASN cc_start: 0.7373 (p0) cc_final: 0.6921 (p0) REVERT: A 152 ILE cc_start: 0.7006 (mm) cc_final: 0.6463 (mm) REVERT: A 216 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5731 (mtp) REVERT: A 281 LYS cc_start: 0.6896 (pttt) cc_final: 0.6422 (tttp) REVERT: A 293 PHE cc_start: 0.6280 (m-80) cc_final: 0.6048 (m-80) REVERT: A 351 LEU cc_start: 0.7686 (mp) cc_final: 0.7406 (mt) REVERT: A 360 THR cc_start: 0.7369 (p) cc_final: 0.7060 (t) REVERT: A 362 ILE cc_start: 0.8495 (pt) cc_final: 0.8252 (pt) REVERT: A 408 ARG cc_start: 0.5726 (mmm-85) cc_final: 0.5341 (tpp80) REVERT: B 93 MET cc_start: 0.6529 (mtt) cc_final: 0.6326 (mtp) REVERT: B 120 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.3741 (ptp) REVERT: B 197 MET cc_start: 0.5252 (mmm) cc_final: 0.5036 (mmm) REVERT: B 281 LYS cc_start: 0.7453 (pttt) cc_final: 0.6375 (tttm) REVERT: B 293 PHE cc_start: 0.6560 (m-80) cc_final: 0.6015 (m-80) REVERT: B 360 THR cc_start: 0.7086 (p) cc_final: 0.6644 (t) REVERT: B 390 LEU cc_start: 0.5945 (tp) cc_final: 0.5491 (tp) REVERT: P 35 THR cc_start: 0.6468 (p) cc_final: 0.6240 (p) REVERT: P 37 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7334 (ptmt) REVERT: P 42 THR cc_start: 0.8214 (m) cc_final: 0.7265 (p) REVERT: P 115 ARG cc_start: 0.6252 (ttp-170) cc_final: 0.4814 (ptt180) REVERT: T 42 THR cc_start: 0.8099 (m) cc_final: 0.7457 (p) REVERT: T 115 ARG cc_start: 0.6170 (ttp-170) cc_final: 0.5448 (ptt180) REVERT: T 133 TYR cc_start: 0.8409 (m-80) cc_final: 0.8192 (m-80) REVERT: f 1196 THR cc_start: 0.9135 (t) cc_final: 0.8867 (p) REVERT: g 1193 ASN cc_start: 0.7819 (m-40) cc_final: 0.7613 (m110) REVERT: V 31 ASP cc_start: 0.7730 (m-30) cc_final: 0.7484 (m-30) REVERT: V 68 ARG cc_start: 0.8056 (mmm-85) cc_final: 0.7827 (mmp80) REVERT: V 105 LYS cc_start: 0.8354 (ptpp) cc_final: 0.7850 (pttp) REVERT: V 188 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8249 (m-40) REVERT: Z 96 LYS cc_start: 0.8032 (mmtt) cc_final: 0.6988 (mmtt) REVERT: b 28 LEU cc_start: 0.8189 (mp) cc_final: 0.7960 (mp) REVERT: b 252 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7213 (mt-10) REVERT: b 298 GLU cc_start: 0.7495 (tt0) cc_final: 0.7194 (tt0) REVERT: b 620 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8610 (ttpp) REVERT: b 918 LEU cc_start: 0.7296 (pp) cc_final: 0.7083 (mm) REVERT: d 9 LYS cc_start: 0.8555 (mttm) cc_final: 0.8186 (tppt) REVERT: d 300 GLU cc_start: 0.7730 (tt0) cc_final: 0.7476 (tt0) REVERT: d 429 GLU cc_start: 0.7599 (mp0) cc_final: 0.7142 (mp0) REVERT: d 798 MET cc_start: 0.8721 (mtp) cc_final: 0.8271 (mtp) REVERT: d 858 PHE cc_start: 0.4396 (m-10) cc_final: 0.3402 (p90) REVERT: c 56 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7918 (mtm-85) outliers start: 254 outliers final: 177 residues processed: 1386 average time/residue: 0.7427 time to fit residues: 1798.8576 Evaluate side-chains 1154 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 964 time to evaluate : 7.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 75 THR Chi-restraints excluded: chain a residue 94 ASP Chi-restraints excluded: chain a residue 109 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 154 GLN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 99 THR Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Y residue 70 LEU Chi-restraints excluded: chain Y residue 108 GLN Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Y residue 186 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 97 ASP Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 108 GLN Chi-restraints excluded: chain W residue 120 GLN Chi-restraints excluded: chain W residue 155 ASP Chi-restraints excluded: chain W residue 160 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 22 MET Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 103 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 188 ASN Chi-restraints excluded: chain V residue 199 SER Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 186 THR Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 378 THR Chi-restraints excluded: chain b residue 437 VAL Chi-restraints excluded: chain b residue 447 SER Chi-restraints excluded: chain b residue 461 ILE Chi-restraints excluded: chain b residue 489 SER Chi-restraints excluded: chain b residue 562 THR Chi-restraints excluded: chain b residue 572 ARG Chi-restraints excluded: chain b residue 620 LYS Chi-restraints excluded: chain b residue 701 ASP Chi-restraints excluded: chain b residue 734 ASN Chi-restraints excluded: chain b residue 745 THR Chi-restraints excluded: chain b residue 761 LEU Chi-restraints excluded: chain b residue 776 ILE Chi-restraints excluded: chain b residue 828 THR Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 879 ILE Chi-restraints excluded: chain b residue 944 VAL Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 378 THR Chi-restraints excluded: chain d residue 447 SER Chi-restraints excluded: chain d residue 499 GLU Chi-restraints excluded: chain d residue 734 ASN Chi-restraints excluded: chain d residue 745 THR Chi-restraints excluded: chain d residue 776 ILE Chi-restraints excluded: chain d residue 828 THR Chi-restraints excluded: chain d residue 843 SER Chi-restraints excluded: chain d residue 879 ILE Chi-restraints excluded: chain c residue 208 SER Chi-restraints excluded: chain c residue 211 SER Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 378 THR Chi-restraints excluded: chain c residue 701 ASP Chi-restraints excluded: chain c residue 745 THR Chi-restraints excluded: chain c residue 776 ILE Chi-restraints excluded: chain c residue 825 SER Chi-restraints excluded: chain c residue 879 ILE Chi-restraints excluded: chain c residue 885 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 472 optimal weight: 6.9990 chunk 263 optimal weight: 0.6980 chunk 707 optimal weight: 0.9990 chunk 578 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 chunk 851 optimal weight: 4.9990 chunk 919 optimal weight: 0.7980 chunk 758 optimal weight: 3.9990 chunk 844 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 683 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: I 27 ASN I 292 ASN F 31 GLN F 151 GLN F 154 GLN Y 104 GLN Y 108 GLN Y 149 ASN O 15 ASN E 151 GLN E 154 GLN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 66 ASN C 151 GLN C 291 ASN U 23 GLN D 318 HIS A 20 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN A 318 HIS ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 HIS B 26 GLN B 83 ASN B 113 HIS ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e1193 ASN e1218 ASN ** b 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 800 GLN c 622 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 75774 Z= 0.172 Angle : 0.521 9.113 102942 Z= 0.278 Chirality : 0.045 0.243 11772 Planarity : 0.004 0.047 13344 Dihedral : 4.826 71.595 10368 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.20 % Allowed : 14.38 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.74 (0.08), residues: 9462 helix: -0.31 (0.16), residues: 1110 sheet: -1.01 (0.09), residues: 3279 loop : -1.41 (0.08), residues: 5073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 144 HIS 0.010 0.001 HIS B 113 PHE 0.025 0.001 PHE d 915 TYR 0.022 0.001 TYR N 133 ARG 0.008 0.000 ARG O 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1134 time to evaluate : 6.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 VAL cc_start: 0.9002 (t) cc_final: 0.8707 (m) REVERT: R 41 LEU cc_start: 0.7659 (mt) cc_final: 0.7315 (tp) REVERT: R 56 ASP cc_start: 0.6374 (p0) cc_final: 0.6127 (m-30) REVERT: R 98 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7132 (ttp-170) REVERT: R 131 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8182 (mttp) REVERT: I 1 MET cc_start: 0.7005 (mtm) cc_final: 0.6529 (mtp) REVERT: I 135 ILE cc_start: 0.8850 (mt) cc_final: 0.8574 (mm) REVERT: I 239 ASN cc_start: 0.8252 (p0) cc_final: 0.7913 (p0) REVERT: I 296 GLU cc_start: 0.7108 (tp30) cc_final: 0.6366 (pt0) REVERT: a 68 ARG cc_start: 0.8288 (mmt90) cc_final: 0.8043 (mmt-90) REVERT: a 155 ASP cc_start: 0.7432 (m-30) cc_final: 0.7190 (m-30) REVERT: Q 6 ARG cc_start: 0.6146 (mmt90) cc_final: 0.4216 (ptp90) REVERT: Q 14 GLU cc_start: 0.7940 (tt0) cc_final: 0.7729 (tt0) REVERT: Q 35 THR cc_start: 0.5035 (p) cc_final: 0.4736 (t) REVERT: Q 140 GLN cc_start: 0.6401 (tp-100) cc_final: 0.5911 (tp40) REVERT: S 10 LEU cc_start: 0.8298 (mt) cc_final: 0.8079 (mt) REVERT: F 224 ILE cc_start: 0.8937 (mm) cc_final: 0.8687 (mm) REVERT: F 382 LYS cc_start: 0.5676 (ttmt) cc_final: 0.5117 (mmtm) REVERT: N 46 LEU cc_start: 0.8186 (pt) cc_final: 0.7878 (pp) REVERT: N 86 THR cc_start: 0.8330 (p) cc_final: 0.7757 (p) REVERT: N 97 ASP cc_start: 0.7356 (t70) cc_final: 0.7037 (t70) REVERT: N 129 GLU cc_start: 0.6472 (pt0) cc_final: 0.6240 (pt0) REVERT: H 1 MET cc_start: 0.7041 (mtm) cc_final: 0.6660 (mtt) REVERT: H 62 SER cc_start: 0.8529 (m) cc_final: 0.8219 (p) REVERT: H 237 PHE cc_start: 0.7983 (t80) cc_final: 0.7524 (t80) REVERT: H 261 LEU cc_start: 0.9028 (mt) cc_final: 0.8806 (mp) REVERT: Y 120 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7862 (mm-40) REVERT: M 6 ARG cc_start: 0.6294 (mmt90) cc_final: 0.4676 (ptt90) REVERT: M 47 ARG cc_start: 0.8223 (ptt180) cc_final: 0.8008 (ptt90) REVERT: M 115 ARG cc_start: 0.7143 (ptm-80) cc_final: 0.6341 (tmm-80) REVERT: O 23 GLN cc_start: 0.6743 (mt0) cc_final: 0.5023 (pm20) REVERT: O 105 LEU cc_start: 0.8536 (tp) cc_final: 0.8328 (tp) REVERT: O 129 GLU cc_start: 0.7996 (pm20) cc_final: 0.7448 (pm20) REVERT: O 131 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8234 (mtmm) REVERT: E 216 MET cc_start: 0.7971 (mmt) cc_final: 0.7095 (mmm) REVERT: E 357 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: E 362 ILE cc_start: 0.8789 (pt) cc_final: 0.8463 (pt) REVERT: C 79 TYR cc_start: 0.4626 (p90) cc_final: 0.4075 (p90) REVERT: C 93 MET cc_start: 0.6062 (mtt) cc_final: 0.5312 (mtp) REVERT: C 126 ASN cc_start: 0.7409 (p0) cc_final: 0.7208 (p0) REVERT: C 197 MET cc_start: 0.5949 (mmp) cc_final: 0.5654 (mmt) REVERT: C 216 MET cc_start: 0.5770 (mmm) cc_final: 0.5530 (mmt) REVERT: C 224 ILE cc_start: 0.6376 (mm) cc_final: 0.6032 (mt) REVERT: C 281 LYS cc_start: 0.7243 (pttt) cc_final: 0.6524 (ttmm) REVERT: C 297 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7709 (mt) REVERT: J 22 MET cc_start: 0.5609 (mtp) cc_final: 0.4786 (mmm) REVERT: J 26 ASP cc_start: 0.3914 (p0) cc_final: 0.2948 (t70) REVERT: J 131 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8017 (mttp) REVERT: L 42 THR cc_start: 0.8273 (m) cc_final: 0.7843 (p) REVERT: L 100 ASN cc_start: 0.7781 (t0) cc_final: 0.7397 (t0) REVERT: L 115 ARG cc_start: 0.5582 (ttp-170) cc_final: 0.4657 (ptt180) REVERT: G 27 ASN cc_start: 0.8374 (t0) cc_final: 0.8164 (t0) REVERT: G 35 GLN cc_start: 0.8535 (mt0) cc_final: 0.8080 (tt0) REVERT: G 62 SER cc_start: 0.8363 (m) cc_final: 0.7929 (p) REVERT: G 143 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7290 (mm-30) REVERT: G 192 GLN cc_start: 0.7710 (tp40) cc_final: 0.7391 (tp40) REVERT: W 2 ARG cc_start: 0.8589 (mtp180) cc_final: 0.8380 (ttt-90) REVERT: U 6 ARG cc_start: 0.5967 (mmt90) cc_final: 0.4517 (ptp90) REVERT: U 115 ARG cc_start: 0.6738 (ptm-80) cc_final: 0.6254 (tmm-80) REVERT: K 28 ASP cc_start: 0.6168 (t70) cc_final: 0.5890 (t70) REVERT: K 103 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: D 1 MET cc_start: 0.6707 (tpp) cc_final: 0.6112 (mmm) REVERT: D 170 SER cc_start: 0.7742 (t) cc_final: 0.7447 (p) REVERT: D 216 MET cc_start: 0.7944 (mmm) cc_final: 0.7594 (mmt) REVERT: D 362 ILE cc_start: 0.8731 (pt) cc_final: 0.8260 (mt) REVERT: A 4 GLN cc_start: 0.6366 (mm-40) cc_final: 0.5958 (mm-40) REVERT: A 61 PHE cc_start: 0.7740 (m-80) cc_final: 0.7527 (m-80) REVERT: A 126 ASN cc_start: 0.7253 (p0) cc_final: 0.6802 (p0) REVERT: A 281 LYS cc_start: 0.7252 (pttt) cc_final: 0.6620 (tttp) REVERT: A 285 LYS cc_start: 0.5166 (pttm) cc_final: 0.4875 (pttm) REVERT: A 342 ASP cc_start: 0.6390 (OUTLIER) cc_final: 0.6039 (t0) REVERT: A 353 PHE cc_start: 0.5741 (m-80) cc_final: 0.5425 (m-80) REVERT: A 360 THR cc_start: 0.7363 (p) cc_final: 0.7142 (t) REVERT: A 362 ILE cc_start: 0.8435 (pt) cc_final: 0.8174 (pt) REVERT: A 408 ARG cc_start: 0.5661 (mmm-85) cc_final: 0.5257 (tpp80) REVERT: B 61 PHE cc_start: 0.8169 (m-80) cc_final: 0.7955 (m-10) REVERT: B 197 MET cc_start: 0.5396 (mmm) cc_final: 0.5155 (mmm) REVERT: B 216 MET cc_start: 0.6054 (mmm) cc_final: 0.5563 (mmm) REVERT: B 281 LYS cc_start: 0.7255 (pttt) cc_final: 0.6771 (tttm) REVERT: B 360 THR cc_start: 0.7097 (p) cc_final: 0.6622 (t) REVERT: P 35 THR cc_start: 0.6395 (p) cc_final: 0.6167 (p) REVERT: P 37 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7384 (ptmt) REVERT: P 42 THR cc_start: 0.8105 (m) cc_final: 0.7228 (p) REVERT: P 102 ARG cc_start: 0.9032 (mmt-90) cc_final: 0.8458 (mmt180) REVERT: P 115 ARG cc_start: 0.6156 (ttp-170) cc_final: 0.4672 (ptt180) REVERT: T 42 THR cc_start: 0.8070 (m) cc_final: 0.7387 (p) REVERT: T 70 ASP cc_start: 0.7565 (t70) cc_final: 0.7156 (t70) REVERT: T 96 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.7715 (mmt180) REVERT: T 115 ARG cc_start: 0.6314 (ttp-170) cc_final: 0.5316 (ptt180) REVERT: f 1196 THR cc_start: 0.9008 (t) cc_final: 0.8794 (p) REVERT: V 68 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7629 (mmm160) REVERT: V 71 GLU cc_start: 0.8580 (tp30) cc_final: 0.8369 (tp30) REVERT: V 105 LYS cc_start: 0.8166 (ptpp) cc_final: 0.7724 (pttp) REVERT: b 125 ASP cc_start: 0.6510 (m-30) cc_final: 0.6306 (m-30) REVERT: b 252 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7222 (mt-10) REVERT: b 620 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8368 (ttpp) REVERT: b 918 LEU cc_start: 0.7304 (pp) cc_final: 0.7047 (mm) REVERT: d 9 LYS cc_start: 0.8474 (mttm) cc_final: 0.8130 (tppt) REVERT: d 300 GLU cc_start: 0.7859 (tt0) cc_final: 0.7590 (tt0) REVERT: d 858 PHE cc_start: 0.4247 (m-10) cc_final: 0.3353 (p90) REVERT: c 184 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.8014 (m) outliers start: 182 outliers final: 124 residues processed: 1243 average time/residue: 0.7177 time to fit residues: 1548.9478 Evaluate side-chains 1112 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 980 time to evaluate : 7.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 18 GLU Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 94 ASP Chi-restraints excluded: chain Q residue 22 MET Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 154 GLN Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Y residue 24 ASP Chi-restraints excluded: chain Y residue 108 GLN Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 97 ASP Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 108 GLN Chi-restraints excluded: chain W residue 120 GLN Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 103 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 447 SER Chi-restraints excluded: chain b residue 461 ILE Chi-restraints excluded: chain b residue 562 THR Chi-restraints excluded: chain b residue 594 ASN Chi-restraints excluded: chain b residue 620 LYS Chi-restraints excluded: chain b residue 701 ASP Chi-restraints excluded: chain b residue 761 LEU Chi-restraints excluded: chain b residue 776 ILE Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 863 VAL Chi-restraints excluded: chain b residue 879 ILE Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 378 THR Chi-restraints excluded: chain d residue 447 SER Chi-restraints excluded: chain d residue 499 GLU Chi-restraints excluded: chain d residue 696 VAL Chi-restraints excluded: chain d residue 701 ASP Chi-restraints excluded: chain d residue 776 ILE Chi-restraints excluded: chain d residue 879 ILE Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 208 SER Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 290 VAL Chi-restraints excluded: chain c residue 378 THR Chi-restraints excluded: chain c residue 447 SER Chi-restraints excluded: chain c residue 465 MET Chi-restraints excluded: chain c residue 701 ASP Chi-restraints excluded: chain c residue 776 ILE Chi-restraints excluded: chain c residue 825 SER Chi-restraints excluded: chain c residue 879 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 841 optimal weight: 5.9990 chunk 640 optimal weight: 1.9990 chunk 441 optimal weight: 4.9990 chunk 94 optimal weight: 0.0770 chunk 406 optimal weight: 5.9990 chunk 571 optimal weight: 0.9990 chunk 854 optimal weight: 5.9990 chunk 904 optimal weight: 0.9990 chunk 446 optimal weight: 1.9990 chunk 809 optimal weight: 3.9990 chunk 243 optimal weight: 0.7980 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 5 ASN F 151 GLN H 27 ASN H 35 GLN Y 149 ASN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN K 140 GLN D 172 ASN A 20 HIS A 41 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 622 GLN d 112 ASN c 506 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 75774 Z= 0.182 Angle : 0.503 8.959 102942 Z= 0.267 Chirality : 0.045 0.202 11772 Planarity : 0.004 0.046 13344 Dihedral : 4.625 70.081 10368 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.75 % Allowed : 15.08 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.63 (0.08), residues: 9462 helix: -0.16 (0.16), residues: 1161 sheet: -0.90 (0.09), residues: 3387 loop : -1.39 (0.08), residues: 4914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 144 HIS 0.011 0.001 HIS A 113 PHE 0.028 0.001 PHE B 255 TYR 0.023 0.001 TYR d 904 ARG 0.007 0.000 ARG O 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18924 Ramachandran restraints generated. 9462 Oldfield, 0 Emsley, 9462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1056 time to evaluate : 8.710 Fit side-chains revert: symmetry clash REVERT: R 11 VAL cc_start: 0.8873 (t) cc_final: 0.8646 (m) REVERT: R 41 LEU cc_start: 0.7757 (mt) cc_final: 0.7466 (tp) REVERT: R 131 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8167 (mttp) REVERT: I 1 MET cc_start: 0.7096 (mtm) cc_final: 0.6564 (mtp) REVERT: I 135 ILE cc_start: 0.8841 (mt) cc_final: 0.8595 (mm) REVERT: I 296 GLU cc_start: 0.7123 (tp30) cc_final: 0.6443 (pt0) REVERT: a 68 ARG cc_start: 0.8295 (mmt90) cc_final: 0.8042 (mmt-90) REVERT: a 120 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8230 (mm-40) REVERT: a 155 ASP cc_start: 0.7451 (m-30) cc_final: 0.7189 (m-30) REVERT: Q 6 ARG cc_start: 0.6153 (mmt90) cc_final: 0.4328 (ptp90) REVERT: Q 35 THR cc_start: 0.5024 (p) cc_final: 0.4746 (t) REVERT: Q 140 GLN cc_start: 0.6331 (tp-100) cc_final: 0.5925 (tp40) REVERT: F 224 ILE cc_start: 0.8978 (mm) cc_final: 0.8750 (mm) REVERT: F 382 LYS cc_start: 0.5891 (ttmt) cc_final: 0.5306 (mmpt) REVERT: N 44 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.4892 (m-10) REVERT: N 46 LEU cc_start: 0.8244 (pt) cc_final: 0.7940 (pp) REVERT: N 86 THR cc_start: 0.8218 (p) cc_final: 0.7808 (p) REVERT: H 1 MET cc_start: 0.7047 (mtm) cc_final: 0.6622 (mtt) REVERT: H 62 SER cc_start: 0.8540 (m) cc_final: 0.8245 (p) REVERT: H 237 PHE cc_start: 0.7977 (t80) cc_final: 0.7498 (t80) REVERT: H 296 GLU cc_start: 0.6689 (tp30) cc_final: 0.6273 (pt0) REVERT: Y 120 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: M 6 ARG cc_start: 0.6297 (mmt90) cc_final: 0.4669 (ptt90) REVERT: M 73 GLN cc_start: 0.8207 (mp10) cc_final: 0.7807 (mp10) REVERT: M 115 ARG cc_start: 0.7110 (ptm-80) cc_final: 0.6333 (tmm-80) REVERT: O 9 ASP cc_start: 0.7879 (m-30) cc_final: 0.7625 (t0) REVERT: O 23 GLN cc_start: 0.6730 (mt0) cc_final: 0.5019 (pm20) REVERT: O 105 LEU cc_start: 0.8591 (tp) cc_final: 0.8355 (tp) REVERT: O 129 GLU cc_start: 0.8056 (pm20) cc_final: 0.7408 (pm20) REVERT: O 131 LYS cc_start: 0.8468 (mtmt) cc_final: 0.7987 (mtmm) REVERT: E 142 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7258 (pttm) REVERT: E 357 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8518 (m-80) REVERT: E 362 ILE cc_start: 0.8892 (pt) cc_final: 0.8586 (pt) REVERT: C 79 TYR cc_start: 0.4619 (p90) cc_final: 0.4132 (p90) REVERT: C 93 MET cc_start: 0.5645 (mtt) cc_final: 0.5309 (mtp) REVERT: C 126 ASN cc_start: 0.7373 (p0) cc_final: 0.7107 (p0) REVERT: C 166 ARG cc_start: 0.4935 (mtm110) cc_final: 0.4538 (mtm110) REVERT: C 197 MET cc_start: 0.5953 (mmp) cc_final: 0.5653 (mmt) REVERT: C 213 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6705 (tp) REVERT: C 224 ILE cc_start: 0.6356 (mm) cc_final: 0.6122 (mt) REVERT: C 281 LYS cc_start: 0.7291 (pttt) cc_final: 0.6545 (ttmm) REVERT: C 297 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7687 (mt) REVERT: J 22 MET cc_start: 0.5650 (mtp) cc_final: 0.4609 (mmm) REVERT: J 26 ASP cc_start: 0.4032 (p0) cc_final: 0.2929 (t70) REVERT: J 70 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6254 (t0) REVERT: J 128 MET cc_start: 0.7936 (mmm) cc_final: 0.7637 (mtt) REVERT: J 131 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8087 (mttp) REVERT: L 1 MET cc_start: 0.4709 (mmt) cc_final: 0.4179 (mmp) REVERT: L 42 THR cc_start: 0.8291 (m) cc_final: 0.7915 (p) REVERT: L 100 ASN cc_start: 0.7802 (t0) cc_final: 0.7407 (t0) REVERT: L 115 ARG cc_start: 0.5616 (ttp-170) cc_final: 0.4668 (ptt180) REVERT: G 16 ASP cc_start: 0.7515 (t0) cc_final: 0.7106 (t0) REVERT: G 27 ASN cc_start: 0.8292 (t0) cc_final: 0.8081 (t0) REVERT: G 35 GLN cc_start: 0.8544 (mt0) cc_final: 0.8130 (tt0) REVERT: G 62 SER cc_start: 0.8404 (m) cc_final: 0.8036 (p) REVERT: G 101 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: G 110 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8987 (mm) REVERT: W 71 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: U 6 ARG cc_start: 0.5876 (mmt90) cc_final: 0.4431 (ptp90) REVERT: U 115 ARG cc_start: 0.6720 (ptm-80) cc_final: 0.6279 (tmm-80) REVERT: D 1 MET cc_start: 0.6715 (tpp) cc_final: 0.6094 (mmm) REVERT: D 170 SER cc_start: 0.7792 (t) cc_final: 0.7489 (p) REVERT: D 216 MET cc_start: 0.7815 (mmm) cc_final: 0.7491 (mmt) REVERT: D 239 TYR cc_start: 0.8446 (m-80) cc_final: 0.8228 (m-80) REVERT: D 362 ILE cc_start: 0.8746 (pt) cc_final: 0.8412 (pt) REVERT: D 443 GLU cc_start: 0.5486 (tp30) cc_final: 0.5250 (tp30) REVERT: A 79 TYR cc_start: 0.4752 (p90) cc_final: 0.4254 (p90) REVERT: A 123 PHE cc_start: 0.6547 (m-80) cc_final: 0.5947 (m-80) REVERT: A 126 ASN cc_start: 0.7289 (p0) cc_final: 0.6822 (p0) REVERT: A 281 LYS cc_start: 0.6927 (pttt) cc_final: 0.6675 (tttp) REVERT: A 334 VAL cc_start: 0.3833 (OUTLIER) cc_final: 0.3508 (p) REVERT: A 360 THR cc_start: 0.7592 (p) cc_final: 0.7325 (t) REVERT: A 408 ARG cc_start: 0.5857 (mmm-85) cc_final: 0.5388 (tpp80) REVERT: B 120 MET cc_start: 0.4746 (OUTLIER) cc_final: 0.3754 (ptm) REVERT: B 197 MET cc_start: 0.5479 (mmm) cc_final: 0.5196 (mmm) REVERT: B 216 MET cc_start: 0.6085 (mmm) cc_final: 0.5557 (mmm) REVERT: P 2 SER cc_start: 0.7103 (t) cc_final: 0.6784 (m) REVERT: P 37 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7364 (ptmt) REVERT: P 42 THR cc_start: 0.8146 (m) cc_final: 0.7297 (p) REVERT: P 102 ARG cc_start: 0.9013 (mmt-90) cc_final: 0.8464 (mmt180) REVERT: P 115 ARG cc_start: 0.6151 (ttp-170) cc_final: 0.4534 (ptt180) REVERT: T 42 THR cc_start: 0.8123 (m) cc_final: 0.7448 (p) REVERT: T 70 ASP cc_start: 0.7589 (t70) cc_final: 0.7140 (t70) REVERT: T 96 ARG cc_start: 0.7885 (mmt-90) cc_final: 0.7660 (mmt180) REVERT: T 115 ARG cc_start: 0.5992 (ttp-170) cc_final: 0.4956 (ptt180) REVERT: f 1196 THR cc_start: 0.9030 (t) cc_final: 0.8803 (p) REVERT: g 1193 ASN cc_start: 0.7838 (m-40) cc_final: 0.7624 (m110) REVERT: V 31 ASP cc_start: 0.7680 (m-30) cc_final: 0.7459 (m-30) REVERT: V 105 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7566 (pttp) REVERT: b 125 ASP cc_start: 0.6605 (m-30) cc_final: 0.6363 (m-30) REVERT: b 298 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: b 620 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8229 (ttpp) REVERT: b 621 GLU cc_start: 0.7460 (tp30) cc_final: 0.7196 (tp30) REVERT: b 918 LEU cc_start: 0.7343 (pp) cc_final: 0.7074 (mm) REVERT: d 9 LYS cc_start: 0.8289 (mttm) cc_final: 0.7956 (tppt) REVERT: d 300 GLU cc_start: 0.7775 (tt0) cc_final: 0.7444 (tt0) REVERT: d 858 PHE cc_start: 0.4467 (m-10) cc_final: 0.3373 (p90) REVERT: c 184 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7926 (m) REVERT: c 886 TYR cc_start: 0.6278 (m-10) cc_final: 0.5929 (m-10) outliers start: 228 outliers final: 167 residues processed: 1205 average time/residue: 0.7636 time to fit residues: 1616.0061 Evaluate side-chains 1138 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 955 time to evaluate : 6.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 94 ASP Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 120 GLN Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 134 ILE Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 154 GLN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 36 SER Chi-restraints excluded: chain N residue 44 PHE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 136 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 99 THR Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Y residue 24 ASP Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 97 ASP Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 128 MET Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain W residue 18 GLU Chi-restraints excluded: chain W residue 39 LYS Chi-restraints excluded: chain W residue 70 LEU Chi-restraints excluded: chain W residue 71 GLU Chi-restraints excluded: chain W residue 77 ASP Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 108 GLN Chi-restraints excluded: chain W residue 120 GLN Chi-restraints excluded: chain U residue 22 MET Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 HIS Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain P residue 93 SER Chi-restraints excluded: chain T residue 26 ASP Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 282 THR Chi-restraints excluded: chain b residue 290 VAL Chi-restraints excluded: chain b residue 298 GLU Chi-restraints excluded: chain b residue 378 THR Chi-restraints excluded: chain b residue 447 SER Chi-restraints excluded: chain b residue 461 ILE Chi-restraints excluded: chain b residue 562 THR Chi-restraints excluded: chain b residue 572 ARG Chi-restraints excluded: chain b residue 594 ASN Chi-restraints excluded: chain b residue 620 LYS Chi-restraints excluded: chain b residue 701 ASP Chi-restraints excluded: chain b residue 745 THR Chi-restraints excluded: chain b residue 761 LEU Chi-restraints excluded: chain b residue 776 ILE Chi-restraints excluded: chain b residue 828 THR Chi-restraints excluded: chain b residue 848 VAL Chi-restraints excluded: chain b residue 879 ILE Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 266 VAL Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 447 SER Chi-restraints excluded: chain d residue 499 GLU Chi-restraints excluded: chain d residue 594 ASN Chi-restraints excluded: chain d residue 696 VAL Chi-restraints excluded: chain d residue 701 ASP Chi-restraints excluded: chain d residue 776 ILE Chi-restraints excluded: chain d residue 828 THR Chi-restraints excluded: chain d residue 879 ILE Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 208 SER Chi-restraints excluded: chain c residue 259 LEU Chi-restraints excluded: chain c residue 266 VAL Chi-restraints excluded: chain c residue 282 THR Chi-restraints excluded: chain c residue 290 VAL Chi-restraints excluded: chain c residue 378 THR Chi-restraints excluded: chain c residue 447 SER Chi-restraints excluded: chain c residue 701 ASP Chi-restraints excluded: chain c residue 745 THR Chi-restraints excluded: chain c residue 776 ILE Chi-restraints excluded: chain c residue 825 SER Chi-restraints excluded: chain c residue 879 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 753 optimal weight: 4.9990 chunk 513 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 673 optimal weight: 1.9990 chunk 373 optimal weight: 5.9990 chunk 772 optimal weight: 4.9990 chunk 625 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 461 optimal weight: 6.9990 chunk 812 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN F 151 GLN F 154 GLN O 140 GLN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 31 GLN A 20 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 5 ASN e1193 ASN ** b 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 622 GLN b 734 ASN d 161 GLN ** d 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 734 ASN ** c 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 622 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4678 Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: