Starting phenix.real_space_refine on Sat Jan 18 22:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kn8_0729/01_2025/6kn8_0729.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kn8_0729/01_2025/6kn8_0729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kn8_0729/01_2025/6kn8_0729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kn8_0729/01_2025/6kn8_0729.map" model { file = "/net/cci-nas-00/data/ceres_data/6kn8_0729/01_2025/6kn8_0729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kn8_0729/01_2025/6kn8_0729.cif" } resolution = 4.8 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= 0.011 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 375 5.16 5 C 38106 2.51 5 N 10360 2.21 5 O 12095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 194 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 60966 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "F" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "H" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "I" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "J" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "K" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "L" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "M" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "N" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "O" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "P" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2207 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'TRANS': 273} Chain: "Q" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2207 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'TRANS': 273} Chain: "R" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "S" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "T" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1101 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'TRANS': 125} Chain breaks: 1 Chain: "U" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1009 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "V" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1273 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain: "W" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2207 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'TRANS': 273} Chain: "X" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2207 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'TRANS': 273} Chain: "Y" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "Z" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "a" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1101 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'TRANS': 125} Chain breaks: 1 Chain: "b" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1009 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "c" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1273 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.53, per 1000 atoms: 0.45 Number of scatterers: 60966 At special positions: 0 Unit cell: (130.98, 170.94, 486.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 375 16.00 P 30 15.00 O 12095 8.00 N 10360 7.00 C 38106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 12.08 Conformation dependent library (CDL) restraints added in 6.2 seconds 15214 Ramachandran restraints generated. 7607 Oldfield, 0 Emsley, 7607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14398 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 75 sheets defined 60.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 113 through 126 Processing helix chain 'A' and resid 137 through 146 removed outlier: 4.057A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.588A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.418A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 113 through 126 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.569A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.124A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.653A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.836A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 196 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 356 removed outlier: 5.267A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.502A pdb=" N GLN D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 196 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.379A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 360 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 113 through 126 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 196 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 268 Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 4.350A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 360 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.251A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 196 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 252 through 260 Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 261 through 262 No H-bonds generated for 'chain 'F' and resid 261 through 262' Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 295 removed outlier: 4.037A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 349 through 356 removed outlier: 5.173A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 93 Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.374A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 196 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 233 through 237 Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 258 through 268 Proline residue: G 264 - end of helix Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 295 removed outlier: 4.179A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 319 Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 349 through 353 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.142A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 196 removed outlier: 3.565A pdb=" N ASP H 187 " --> pdb=" O ARG H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 233 through 237 Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 295 removed outlier: 4.506A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 319 removed outlier: 3.567A pdb=" N GLN H 314 " --> pdb=" O ALA H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 Processing helix chain 'H' and resid 349 through 353 Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 112 through 126 removed outlier: 4.138A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 196 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 233 through 237 Processing helix chain 'I' and resid 252 through 260 Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 261 through 262 No H-bonds generated for 'chain 'I' and resid 261 through 262' Processing helix chain 'I' and resid 263 through 268 Processing helix chain 'I' and resid 273 through 284 Processing helix chain 'I' and resid 286 through 295 removed outlier: 3.924A pdb=" N LYS I 291 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASP I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 337 through 348 Processing helix chain 'I' and resid 349 through 353 Processing helix chain 'I' and resid 360 through 366 Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 78 through 93 Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 113 through 126 Processing helix chain 'J' and resid 137 through 146 Processing helix chain 'J' and resid 172 through 175 Processing helix chain 'J' and resid 181 through 196 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 222 through 231 Processing helix chain 'J' and resid 233 through 237 Processing helix chain 'J' and resid 252 through 260 Proline residue: J 258 - end of helix Processing helix chain 'J' and resid 261 through 262 No H-bonds generated for 'chain 'J' and resid 261 through 262' Processing helix chain 'J' and resid 263 through 268 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 289 through 295 Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 337 through 348 Processing helix chain 'J' and resid 349 through 353 Processing helix chain 'J' and resid 360 through 366 Processing helix chain 'J' and resid 369 through 374 Processing helix chain 'K' and resid 55 through 61 Processing helix chain 'K' and resid 78 through 93 removed outlier: 3.618A pdb=" N GLU K 93 " --> pdb=" O THR K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 101 Processing helix chain 'K' and resid 112 through 126 removed outlier: 4.210A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 196 removed outlier: 3.537A pdb=" N ASP K 187 " --> pdb=" O ARG K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 222 through 231 Processing helix chain 'K' and resid 233 through 237 Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 289 through 294 removed outlier: 3.512A pdb=" N LEU K 293 " --> pdb=" O ILE K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 348 Processing helix chain 'K' and resid 349 through 353 Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 369 through 374 Processing helix chain 'L' and resid 55 through 61 Processing helix chain 'L' and resid 78 through 92 Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 112 through 126 removed outlier: 4.236A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 146 Processing helix chain 'L' and resid 172 through 175 Processing helix chain 'L' and resid 181 through 196 removed outlier: 3.520A pdb=" N ASP L 187 " --> pdb=" O ARG L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 222 through 231 Processing helix chain 'L' and resid 233 through 237 Processing helix chain 'L' and resid 252 through 263 Proline residue: L 258 - end of helix removed outlier: 4.248A pdb=" N LEU L 261 " --> pdb=" O CYS L 257 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE L 262 " --> pdb=" O PRO L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 268 Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 286 through 295 removed outlier: 4.093A pdb=" N LYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 319 Processing helix chain 'L' and resid 337 through 349 Processing helix chain 'L' and resid 350 through 356 removed outlier: 5.285A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 369 through 374 Processing helix chain 'M' and resid 55 through 61 Processing helix chain 'M' and resid 78 through 91 Processing helix chain 'M' and resid 97 through 101 Processing helix chain 'M' and resid 112 through 126 removed outlier: 4.191A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 Processing helix chain 'M' and resid 172 through 175 Processing helix chain 'M' and resid 181 through 196 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 222 through 231 Processing helix chain 'M' and resid 233 through 237 Processing helix chain 'M' and resid 252 through 260 Proline residue: M 258 - end of helix Processing helix chain 'M' and resid 261 through 268 Proline residue: M 264 - end of helix Processing helix chain 'M' and resid 273 through 284 Processing helix chain 'M' and resid 286 through 295 removed outlier: 5.291A pdb=" N ASP M 292 " --> pdb=" O ASP M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 319 Processing helix chain 'M' and resid 337 through 348 Processing helix chain 'M' and resid 349 through 355 removed outlier: 3.633A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 369 through 374 Processing helix chain 'N' and resid 55 through 61 Processing helix chain 'N' and resid 78 through 91 Processing helix chain 'N' and resid 97 through 101 Processing helix chain 'N' and resid 112 through 126 removed outlier: 4.185A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 146 Processing helix chain 'N' and resid 172 through 175 Processing helix chain 'N' and resid 181 through 196 Processing helix chain 'N' and resid 202 through 217 Processing helix chain 'N' and resid 222 through 231 Processing helix chain 'N' and resid 233 through 237 Processing helix chain 'N' and resid 252 through 263 Proline residue: N 258 - end of helix removed outlier: 4.241A pdb=" N LEU N 261 " --> pdb=" O CYS N 257 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE N 262 " --> pdb=" O PRO N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 268 Processing helix chain 'N' and resid 273 through 284 Processing helix chain 'N' and resid 286 through 294 removed outlier: 3.846A pdb=" N LYS N 291 " --> pdb=" O ILE N 287 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP N 292 " --> pdb=" O ASP N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 319 Processing helix chain 'N' and resid 337 through 348 Processing helix chain 'N' and resid 349 through 353 Processing helix chain 'N' and resid 360 through 366 Processing helix chain 'N' and resid 369 through 374 Processing helix chain 'O' and resid 55 through 61 Processing helix chain 'O' and resid 78 through 93 removed outlier: 3.942A pdb=" N GLU O 93 " --> pdb=" O THR O 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 101 Processing helix chain 'O' and resid 112 through 126 removed outlier: 4.177A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.762A pdb=" N SER O 141 " --> pdb=" O GLN O 137 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU O 142 " --> pdb=" O ALA O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 175 Processing helix chain 'O' and resid 181 through 196 Processing helix chain 'O' and resid 202 through 217 Processing helix chain 'O' and resid 222 through 231 Processing helix chain 'O' and resid 233 through 237 Processing helix chain 'O' and resid 252 through 263 Proline residue: O 258 - end of helix removed outlier: 4.690A pdb=" N LEU O 261 " --> pdb=" O CYS O 257 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE O 262 " --> pdb=" O PRO O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 268 Processing helix chain 'O' and resid 273 through 284 Processing helix chain 'O' and resid 286 through 295 removed outlier: 4.083A pdb=" N LYS O 291 " --> pdb=" O ILE O 287 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASP O 292 " --> pdb=" O ASP O 288 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA O 295 " --> pdb=" O LYS O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 321 Processing helix chain 'O' and resid 337 through 348 removed outlier: 3.530A pdb=" N ILE O 341 " --> pdb=" O TYR O 337 " (cutoff:3.500A) Processing helix chain 'O' and resid 349 through 353 Processing helix chain 'O' and resid 360 through 366 Processing helix chain 'O' and resid 369 through 374 Processing helix chain 'P' and resid 12 through 281 Processing helix chain 'Q' and resid 13 through 282 removed outlier: 3.925A pdb=" N ALA Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 28 Processing helix chain 'S' and resid 1 through 29 Processing helix chain 'T' and resid 100 through 149 Processing helix chain 'T' and resid 200 through 215 Processing helix chain 'T' and resid 225 through 271 Processing helix chain 'U' and resid 42 through 80 Processing helix chain 'U' and resid 89 through 136 Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'U' and resid 161 through 163 No H-bonds generated for 'chain 'U' and resid 161 through 163' Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 13 through 28 Processing helix chain 'V' and resid 37 through 48 Processing helix chain 'V' and resid 53 through 63 Processing helix chain 'V' and resid 73 through 84 Processing helix chain 'V' and resid 93 through 105 removed outlier: 3.636A pdb=" N MET V 103 " --> pdb=" O ASP V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 123 Processing helix chain 'V' and resid 129 through 141 Processing helix chain 'V' and resid 149 through 157 Processing helix chain 'W' and resid 12 through 281 Processing helix chain 'X' and resid 13 through 282 removed outlier: 3.924A pdb=" N ALA X 269 " --> pdb=" O LEU X 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1 through 28 Processing helix chain 'Z' and resid 1 through 29 Processing helix chain 'a' and resid 100 through 149 Processing helix chain 'a' and resid 200 through 215 Processing helix chain 'a' and resid 225 through 271 Processing helix chain 'b' and resid 42 through 80 Processing helix chain 'b' and resid 89 through 136 Processing helix chain 'b' and resid 150 through 160 Processing helix chain 'b' and resid 161 through 163 No H-bonds generated for 'chain 'b' and resid 161 through 163' Processing helix chain 'c' and resid 3 through 11 Processing helix chain 'c' and resid 13 through 28 Processing helix chain 'c' and resid 37 through 48 Processing helix chain 'c' and resid 53 through 63 Processing helix chain 'c' and resid 73 through 84 Processing helix chain 'c' and resid 93 through 105 removed outlier: 3.636A pdb=" N MET c 103 " --> pdb=" O ASP c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 123 Processing helix chain 'c' and resid 129 through 141 Processing helix chain 'c' and resid 149 through 157 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.507A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 5.880A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.306A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.950A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.487A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.469A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.566A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 removed outlier: 5.790A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.515A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 5.807A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.509A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD2, first strand: chain 'F' and resid 169 through 170 removed outlier: 5.794A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.404A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.807A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD9, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.218A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE2, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.515A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AE5, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.338A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA I 135 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AE7, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AE8, first strand: chain 'I' and resid 169 through 170 removed outlier: 5.625A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AF1, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.155A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N CYS J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA J 135 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AF3, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AF4, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AF6, first strand: chain 'K' and resid 29 through 31 removed outlier: 6.452A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N CYS K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR K 103 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA K 135 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU K 105 " --> pdb=" O ALA K 135 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AF8, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AF9, first strand: chain 'K' and resid 169 through 170 removed outlier: 6.590A pdb=" N ASN K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AG2, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.549A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N CYS L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR L 103 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA L 135 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU L 105 " --> pdb=" O ALA L 135 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AG4, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AG5, first strand: chain 'L' and resid 169 through 170 removed outlier: 5.795A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN L 297 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AG7, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.713A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR M 103 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA M 135 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU M 105 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AG9, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AH1, first strand: chain 'M' and resid 169 through 170 removed outlier: 5.753A pdb=" N ILE M 151 " --> pdb=" O VAL M 298 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN M 297 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 238 through 241 Processing sheet with id=AH3, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.240A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR N 103 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA N 135 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU N 105 " --> pdb=" O ALA N 135 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AH5, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AH6, first strand: chain 'N' and resid 169 through 170 removed outlier: 5.780A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN N 297 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 238 through 241 Processing sheet with id=AH8, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.233A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR O 103 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA O 135 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU O 105 " --> pdb=" O ALA O 135 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 53 through 54 Processing sheet with id=AI1, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AI2, first strand: chain 'O' and resid 169 through 170 removed outlier: 3.517A pdb=" N VAL O 163 " --> pdb=" O VAL O 152 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN O 297 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 238 through 241 3699 hydrogen bonds defined for protein. 10206 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: 23.78 Time building geometry restraints manager: 14.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 11024 1.31 - 1.44: 16372 1.44 - 1.58: 33667 1.58 - 1.72: 303 1.72 - 1.85: 655 Bond restraints: 62021 Sorted by residual: bond pdb=" CB HIS D 161 " pdb=" CG HIS D 161 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.99e+01 bond pdb=" SD MET S 8 " pdb=" CE MET S 8 " ideal model delta sigma weight residual 1.791 1.634 0.157 2.50e-02 1.60e+03 3.95e+01 bond pdb=" SD MET Z 8 " pdb=" CE MET Z 8 " ideal model delta sigma weight residual 1.791 1.634 0.157 2.50e-02 1.60e+03 3.94e+01 bond pdb=" CA ILE R 4 " pdb=" CB ILE R 4 " ideal model delta sigma weight residual 1.544 1.467 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" CA ILE Y 4 " pdb=" CB ILE Y 4 " ideal model delta sigma weight residual 1.544 1.467 0.077 1.26e-02 6.30e+03 3.75e+01 ... (remaining 62016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 80937 4.27 - 8.55: 2636 8.55 - 12.82: 158 12.82 - 17.10: 21 17.10 - 21.37: 5 Bond angle restraints: 83757 Sorted by residual: angle pdb=" N VAL N 163 " pdb=" CA VAL N 163 " pdb=" C VAL N 163 " ideal model delta sigma weight residual 107.56 117.54 -9.98 9.10e-01 1.21e+00 1.20e+02 angle pdb=" C ALA N 331 " pdb=" N PRO N 332 " pdb=" CA PRO N 332 " ideal model delta sigma weight residual 119.66 126.93 -7.27 7.20e-01 1.93e+00 1.02e+02 angle pdb=" N VAL L 163 " pdb=" CA VAL L 163 " pdb=" C VAL L 163 " ideal model delta sigma weight residual 107.89 117.52 -9.63 1.09e+00 8.42e-01 7.81e+01 angle pdb=" C GLN C 263 " pdb=" N PRO C 264 " pdb=" CA PRO C 264 " ideal model delta sigma weight residual 119.82 128.24 -8.42 9.80e-01 1.04e+00 7.37e+01 angle pdb=" C GLN N 263 " pdb=" N PRO N 264 " pdb=" CA PRO N 264 " ideal model delta sigma weight residual 119.56 128.19 -8.63 1.02e+00 9.61e-01 7.16e+01 ... (remaining 83752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 37552 35.85 - 71.71: 510 71.71 - 107.56: 41 107.56 - 143.41: 15 143.41 - 179.26: 10 Dihedral angle restraints: 38128 sinusoidal: 15816 harmonic: 22312 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.74 179.26 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP M 401 " pdb=" O3A ADP M 401 " pdb=" PB ADP M 401 " pdb=" PA ADP M 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.14 -175.15 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.70 -172.71 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 38125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 6428 0.096 - 0.193: 2272 0.193 - 0.289: 483 0.289 - 0.385: 76 0.385 - 0.482: 14 Chirality restraints: 9273 Sorted by residual: chirality pdb=" C3' ADP M 401 " pdb=" C2' ADP M 401 " pdb=" C4' ADP M 401 " pdb=" O3' ADP M 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.99 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CB ILE R 4 " pdb=" CA ILE R 4 " pdb=" CG1 ILE R 4 " pdb=" CG2 ILE R 4 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CB ILE Y 4 " pdb=" CA ILE Y 4 " pdb=" CG1 ILE Y 4 " pdb=" CG2 ILE Y 4 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 9270 not shown) Planarity restraints: 10873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP E 401 " -0.530 2.00e-02 2.50e+03 2.14e-01 1.26e+03 pdb=" C2 ADP E 401 " 0.108 2.00e-02 2.50e+03 pdb=" C4 ADP E 401 " 0.120 2.00e-02 2.50e+03 pdb=" C5 ADP E 401 " 0.037 2.00e-02 2.50e+03 pdb=" C6 ADP E 401 " -0.077 2.00e-02 2.50e+03 pdb=" C8 ADP E 401 " 0.225 2.00e-02 2.50e+03 pdb=" N1 ADP E 401 " -0.022 2.00e-02 2.50e+03 pdb=" N3 ADP E 401 " 0.145 2.00e-02 2.50e+03 pdb=" N6 ADP E 401 " -0.282 2.00e-02 2.50e+03 pdb=" N7 ADP E 401 " 0.117 2.00e-02 2.50e+03 pdb=" N9 ADP E 401 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP J 401 " -0.508 2.00e-02 2.50e+03 2.02e-01 1.12e+03 pdb=" C2 ADP J 401 " 0.084 2.00e-02 2.50e+03 pdb=" C4 ADP J 401 " 0.133 2.00e-02 2.50e+03 pdb=" C5 ADP J 401 " 0.036 2.00e-02 2.50e+03 pdb=" C6 ADP J 401 " -0.072 2.00e-02 2.50e+03 pdb=" C8 ADP J 401 " 0.196 2.00e-02 2.50e+03 pdb=" N1 ADP J 401 " -0.038 2.00e-02 2.50e+03 pdb=" N3 ADP J 401 " 0.154 2.00e-02 2.50e+03 pdb=" N6 ADP J 401 " -0.245 2.00e-02 2.50e+03 pdb=" N7 ADP J 401 " 0.089 2.00e-02 2.50e+03 pdb=" N9 ADP J 401 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP I 401 " -0.481 2.00e-02 2.50e+03 1.91e-01 1.00e+03 pdb=" C2 ADP I 401 " 0.046 2.00e-02 2.50e+03 pdb=" C4 ADP I 401 " 0.148 2.00e-02 2.50e+03 pdb=" C5 ADP I 401 " 0.049 2.00e-02 2.50e+03 pdb=" C6 ADP I 401 " -0.058 2.00e-02 2.50e+03 pdb=" C8 ADP I 401 " 0.164 2.00e-02 2.50e+03 pdb=" N1 ADP I 401 " -0.050 2.00e-02 2.50e+03 pdb=" N3 ADP I 401 " 0.157 2.00e-02 2.50e+03 pdb=" N6 ADP I 401 " -0.222 2.00e-02 2.50e+03 pdb=" N7 ADP I 401 " 0.070 2.00e-02 2.50e+03 pdb=" N9 ADP I 401 " 0.177 2.00e-02 2.50e+03 ... (remaining 10870 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 9009 2.75 - 3.29: 64091 3.29 - 3.82: 105634 3.82 - 4.36: 142120 4.36 - 4.90: 219259 Nonbonded interactions: 540113 Sorted by model distance: nonbonded pdb=" NZ LYS X 268 " pdb=" OE1 GLU a 117 " model vdw 2.211 3.120 nonbonded pdb=" NZ LYS Q 268 " pdb=" OE1 GLU T 117 " model vdw 2.211 3.120 nonbonded pdb=" CG LYS M 213 " pdb=" OH TYR M 306 " model vdw 2.217 3.440 nonbonded pdb=" NZ LYS I 326 " pdb=" OD1 ASP Q 219 " model vdw 2.223 3.120 nonbonded pdb=" CB ASP F 25 " pdb=" O LEU U 144 " model vdw 2.232 3.440 ... (remaining 540108 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'T' selection = chain 'a' } ncs_group { reference = chain 'U' selection = chain 'b' } ncs_group { reference = chain 'V' selection = chain 'c' } Set up NCS constraints Number of NCS constrained groups: 6 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' } pdb_interpretation.ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'Y' selection = chain 'Z' } pdb_interpretation.ncs_group { reference = chain 'T' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'U' selection = chain 'b' } pdb_interpretation.ncs_group { reference = chain 'V' selection = chain 'c' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.690 Check model and map are aligned: 0.340 Set scattering table: 0.440 Process input model: 106.390 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4426 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 : 0.019 0.157 62021 Z= 1.223 Angle : 1.813 21.372 83757 Z= 1.226 Chirality : 0.102 0.482 9273 Planarity : 0.011 0.214 10873 Dihedral : 12.391 179.264 23730 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.02 % Favored : 97.44 % Rotamer: Outliers : 0.41 % Allowed : 1.41 % Favored : 98.18 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.09), residues: 7607 helix: -0.67 (0.07), residues: 4083 sheet: 0.55 (0.20), residues: 650 loop : 0.83 (0.12), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.014 TRP N 340 HIS 0.021 0.002 HIS H 161 PHE 0.039 0.006 PHE V 156 TYR 0.114 0.009 TYR L 166 ARG 0.012 0.001 ARG O 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15214 Ramachandran restraints generated. 7607 Oldfield, 0 Emsley, 7607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15214 Ramachandran restraints generated. 7607 Oldfield, 0 Emsley, 7607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.8793 (mt) cc_final: 0.8431 (mp) REVERT: A 289 ILE cc_start: 0.8010 (mt) cc_final: 0.7238 (mm) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1317 time to fit residues: 6.9580 Evaluate side-chains 30 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.256 Evaluate side-chains 9 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.203 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1213 time to fit residues: 1.5460 Evaluate side-chains 5 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.202 Evaluate side-chains 3 residues out of total 25 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.023 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0849 time to fit residues: 0.2982 Evaluate side-chains 3 residues out of total 25 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.023 Evaluate side-chains 2 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.105 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4233 time to fit residues: 1.0298 Evaluate side-chains 0 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.106 Evaluate side-chains 4 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.135 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2300 time to fit residues: 1.0945 Evaluate side-chains 2 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.092 Evaluate side-chains 13 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0772 time to fit residues: 1.2928 Evaluate side-chains 11 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 637 optimal weight: 0.5980 chunk 572 optimal weight: 0.9980 chunk 317 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 386 optimal weight: 0.0970 chunk 305 optimal weight: 6.9990 chunk 591 optimal weight: 9.9990 chunk 229 optimal weight: 0.0010 chunk 359 optimal weight: 0.4980 chunk 440 optimal weight: 1.9990 chunk 685 optimal weight: 0.0470 overall best weight: 0.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 49 GLN K 101 HIS ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 153 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 48 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.061679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.044805 restraints weight = 21550.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.046010 restraints weight = 17508.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.046983 restraints weight = 14652.209| |-----------------------------------------------------------------------------| r_work (final): 0.3382 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.066754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.059923 restraints weight = 26258.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.060239 restraints weight = 23383.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.060477 restraints weight = 21339.039| |-----------------------------------------------------------------------------| r_work (final): 0.3678 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.041477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.037719 restraints weight = 5545.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.038370 restraints weight = 2904.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.038766 restraints weight = 1750.872| |-----------------------------------------------------------------------------| r_work (final): 0.3211 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.239943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.175317 restraints weight = 13308.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.174118 restraints weight = 12530.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.174106 restraints weight = 12439.084| |-----------------------------------------------------------------------------| r_work (final): 0.4481 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.059597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.057218 restraints weight = 256208.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.057017 restraints weight = 176650.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.056918 restraints weight = 189197.792| |-----------------------------------------------------------------------------| r_work (final): 0.3476 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.065217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.057384 restraints weight = 26898.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.057384 restraints weight = 26934.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.057384 restraints weight = 26934.391| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4337 moved from start: 2.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.100 1.513 62021 Z= 6.290 Angle : 3.823 57.741 83757 Z= 2.319 Chirality : 0.236 2.395 9273 Planarity : 0.019 0.438 10873 Dihedral : 14.061 172.449 8514 Min Nonbonded Distance : 0.885 Molprobity Statistics. All-atom Clashscore : 185.32 Ramachandran Plot: Outliers : 6.32 % Allowed : 6.55 % Favored : 87.13 % Rotamer: Outliers : 7.28 % Allowed : 4.33 % Favored : 88.40 % Cbeta Deviations : 14.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.81 % 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: -1.66 (0.09), residues: 7607 helix: -1.61 (0.08), residues: 3772 sheet: 0.04 (0.20), residues: 720 loop : -0.43 (0.11), residues: 3115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP G 86 HIS 0.051 0.002 HIS P 276 PHE 0.121 0.006 PHE T 248 TYR 0.151 0.006 TYR Q 162 ARG 0.086 0.003 ARG b 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14444 Ramachandran restraints generated. 7222 Oldfield, 0 Emsley, 7222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14444 Ramachandran restraints generated. 7222 Oldfield, 0 Emsley, 7222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 189 LEU cc_start: 0.9756 (tp) cc_final: 0.9387 (tt) REVERT: K 190 MET cc_start: 0.8773 (mmm) cc_final: 0.8500 (mmm) REVERT: K 200 PHE cc_start: 0.6895 (m-10) cc_final: 0.6358 (m-80) REVERT: K 210 ARG cc_start: 0.9342 (ptm160) cc_final: 0.9138 (ppt170) REVERT: K 213 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8668 (mtpt) REVERT: K 299 MET cc_start: 0.7882 (ptm) cc_final: 0.7231 (ppp) REVERT: K 309 ILE cc_start: 0.8238 (tt) cc_final: 0.7175 (tt) REVERT: K 313 MET cc_start: 0.9835 (mmp) cc_final: 0.9361 (mmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1639 time to fit residues: 9.8107 Evaluate side-chains 36 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.252 Evaluate side-chains 146 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 36 time to evaluate : 0.205 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: symmetry clash REVERT: Q 47 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8796 (mp10) REVERT: Q 69 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8933 (tm-30) REVERT: Q 73 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8745 (mt) REVERT: Q 111 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7393 (mm-40) REVERT: Q 176 LEU cc_start: 0.1769 (OUTLIER) cc_final: -0.2127 (mp) REVERT: Q 199 THR cc_start: 0.5806 (OUTLIER) cc_final: 0.5564 (p) REVERT: Q 202 ASN cc_start: 0.8638 (m-40) cc_final: 0.8268 (m-40) REVERT: Q 228 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8912 (tt) REVERT: Q 230 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8976 (m-30) REVERT: Q 231 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8575 (tmtt) REVERT: Q 249 LEU cc_start: 0.4957 (OUTLIER) cc_final: 0.4638 (tt) outliers start: 110 outliers final: 19 residues processed: 130 average time/residue: 0.1652 time to fit residues: 23.6327 Evaluate side-chains 56 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 27 time to evaluate : 0.202 Evaluate side-chains 4 residues out of total 25 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.024 Fit side-chains revert: symmetry clash REVERT: R 1 MET cc_start: -0.4850 (mpp) cc_final: -0.5226 (mtt) outliers start: 1 outliers final: 0 residues processed: 4 average time/residue: 0.1459 time to fit residues: 0.6294 Evaluate side-chains 3 residues out of total 25 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.023 Evaluate side-chains 9 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 3 time to evaluate : 0.097 Fit side-chains REVERT: a 146 LYS cc_start: -0.5154 (OUTLIER) cc_final: -0.6152 (pttp) REVERT: a 250 LEU cc_start: 0.8694 (mt) cc_final: 0.8297 (tt) outliers start: 6 outliers final: 0 residues processed: 9 average time/residue: 0.1577 time to fit residues: 1.6526 Evaluate side-chains 2 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1 time to evaluate : 0.096 Evaluate side-chains 4 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.093 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 4 average time/residue: 0.1625 time to fit residues: 0.8241 Evaluate side-chains 3 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.093 Evaluate side-chains 23 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: c 139 ASP cc_start: 0.9488 (OUTLIER) cc_final: 0.8941 (t0) outliers start: 9 outliers final: 0 residues processed: 22 average time/residue: 0.1025 time to fit residues: 2.6178 Evaluate side-chains 13 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 673 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 320 optimal weight: 8.9990 chunk 753 optimal weight: 5.9990 chunk 470 optimal weight: 0.7980 chunk 399 optimal weight: 10.0000 chunk 30 optimal weight: 0.0030 chunk 134 optimal weight: 10.0000 chunk 676 optimal weight: 4.9990 chunk 456 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 12 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 17 ASN Q 103 GLN Q 153 HIS ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 263 GLN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 271 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.044894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.036592 restraints weight = 39387.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.037338 restraints weight = 31383.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.037904 restraints weight = 26410.001| |-----------------------------------------------------------------------------| r_work (final): 0.3162 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.076921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.071222 restraints weight = 28439.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.071362 restraints weight = 27304.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.071463 restraints weight = 26267.828| |-----------------------------------------------------------------------------| r_work (final): 0.3804 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.055692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.048965 restraints weight = 2465.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.048965 restraints weight = 2451.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.048965 restraints weight = 2451.381| |-----------------------------------------------------------------------------| r_work (final): 0.3150 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.237942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.173775 restraints weight = 14517.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.172523 restraints weight = 17818.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.172059 restraints weight = 15345.209| |-----------------------------------------------------------------------------| r_work (final): 0.4440 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.060251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.059982 restraints weight = 24530.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.059014 restraints weight = 47217.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.058781 restraints weight = 66650.854| |-----------------------------------------------------------------------------| r_work (final): 0.3571 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.065457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.062331 restraints weight = 29245.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.062331 restraints weight = 31128.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.062331 restraints weight = 31128.684| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 2.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.095 1.433 62021 Z= 5.997 Angle : 4.057 49.085 83757 Z= 2.388 Chirality : 0.241 2.288 9273 Planarity : 0.019 0.390 10873 Dihedral : 14.278 172.233 8514 Min Nonbonded Distance : 0.887 Molprobity Statistics. All-atom Clashscore : 194.86 Ramachandran Plot: Outliers : 7.02 % Allowed : 7.05 % Favored : 85.93 % Rotamer: Outliers : 7.44 % Allowed : 5.12 % Favored : 87.44 % Cbeta Deviations : 14.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.92 % 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: -1.95 (0.09), residues: 7607 helix: -1.63 (0.08), residues: 3721 sheet: 0.46 (0.19), residues: 675 loop : -1.06 (0.11), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.007 TRP F 86 HIS 0.051 0.004 HIS Q 276 PHE 0.082 0.004 PHE T 248 TYR 0.193 0.012 TYR P 221 ARG 0.075 0.003 ARG Q 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13698 Ramachandran restraints generated. 6849 Oldfield, 0 Emsley, 6849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13698 Ramachandran restraints generated. 6849 Oldfield, 0 Emsley, 6849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 119 MET cc_start: 0.9389 (ptm) cc_final: 0.9037 (ppp) outliers start: 3 outliers final: 0 residues processed: 24 average time/residue: 0.1702 time to fit residues: 4.9869 Evaluate side-chains 17 residues out of total 318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.259 Evaluate side-chains 126 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 28 time to evaluate : 0.206 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: symmetry clash REVERT: Q 15 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9091 (mmmt) REVERT: Q 69 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: Q 105 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6648 (tmm160) REVERT: Q 111 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6383 (mm-40) REVERT: Q 122 GLU cc_start: 0.1892 (OUTLIER) cc_final: 0.1407 (mp0) REVERT: Q 147 GLN cc_start: 0.4823 (OUTLIER) cc_final: 0.4078 (pp30) REVERT: Q 214 TYR cc_start: -0.0276 (OUTLIER) cc_final: -0.0935 (t80) REVERT: Q 230 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8714 (m-30) REVERT: Q 256 LEU cc_start: 0.3014 (OUTLIER) cc_final: 0.2409 (tp) outliers start: 98 outliers final: 30 residues processed: 114 average time/residue: 0.1608 time to fit residues: 20.3067 Evaluate side-chains 59 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 20 time to evaluate : 0.201 Evaluate side-chains 4 residues out of total 25 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.024 Fit side-chains revert: symmetry clash REVERT: R 1 MET cc_start: -0.5101 (mpp) cc_final: -0.5664 (mtt) outliers start: 1 outliers final: 0 residues processed: 4 average time/residue: 0.1553 time to fit residues: 0.6677 Evaluate side-chains 3 residues out of total 25 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.024 Evaluate side-chains 11 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: a 146 LYS cc_start: -0.6420 (OUTLIER) cc_final: -0.7459 (pttp) REVERT: a 253 LYS cc_start: 0.5738 (OUTLIER) cc_final: 0.5432 (tmtt) outliers start: 10 outliers final: 2 residues processed: 11 average time/residue: 0.2168 time to fit residues: 2.6338 Evaluate side-chains 5 residues out of total 117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1 time to evaluate : 0.096 Evaluate side-chains 4 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 2 time to evaluate : 0.093 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 4 average time/residue: 0.0604 time to fit residues: 0.4150 Evaluate side-chains 2 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.092 Evaluate side-chains 23 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 12 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 37 SER cc_start: 0.1817 (OUTLIER) cc_final: 0.1459 (m) outliers start: 11 outliers final: 2 residues processed: 22 average time/residue: 0.0792 time to fit residues: 2.1022 Evaluate side-chains 13 residues out of total 141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7976 > 50: distance: 0 - 1: 48.844 distance: 1 - 2: 44.958 distance: 1 - 4: 15.324 distance: 2 - 3: 8.132 distance: 2 - 8: 63.082 distance: 4 - 5: 24.117 distance: 4 - 6: 22.223 distance: 5 - 7: 33.471 distance: 8 - 9: 36.744 distance: 9 - 10: 25.829 distance: 10 - 11: 18.788 distance: 10 - 12: 41.360 distance: 12 - 13: 4.748 distance: 13 - 14: 15.294 distance: 13 - 16: 27.279 distance: 14 - 15: 6.411 distance: 14 - 20: 16.893 distance: 15 - 51: 7.722 distance: 16 - 17: 55.140 distance: 17 - 18: 40.091 distance: 17 - 19: 44.944 distance: 20 - 21: 56.594 distance: 21 - 22: 4.276 distance: 21 - 24: 9.855 distance: 22 - 23: 49.786 distance: 22 - 29: 48.800 distance: 23 - 62: 69.049 distance: 24 - 25: 13.379 distance: 25 - 26: 56.706 distance: 26 - 27: 60.438 distance: 30 - 31: 33.081 distance: 30 - 33: 46.792 distance: 31 - 32: 6.340 distance: 31 - 40: 7.311 distance: 33 - 34: 42.211 distance: 34 - 35: 35.197 distance: 35 - 36: 19.643 distance: 36 - 37: 38.515 distance: 37 - 38: 7.534 distance: 37 - 39: 30.785 distance: 40 - 41: 38.536 distance: 41 - 42: 66.149 distance: 41 - 44: 37.730 distance: 42 - 43: 49.406 distance: 42 - 51: 3.947 distance: 44 - 45: 19.254 distance: 45 - 46: 32.024 distance: 45 - 47: 25.816 distance: 46 - 48: 49.987 distance: 47 - 49: 45.831 distance: 51 - 52: 40.125 distance: 52 - 53: 21.959 distance: 52 - 55: 29.854 distance: 53 - 54: 36.921 distance: 53 - 62: 18.189 distance: 55 - 56: 41.380 distance: 56 - 57: 39.249 distance: 57 - 58: 20.084 distance: 58 - 59: 30.980 distance: 59 - 60: 46.524 distance: 59 - 61: 16.924 distance: 62 - 63: 55.852 distance: 63 - 64: 48.776 distance: 64 - 65: 40.755 distance: 64 - 68: 42.081 distance: 68 - 69: 40.048 distance: 68 - 74: 62.901 distance: 69 - 70: 19.393 distance: 69 - 72: 40.515 distance: 70 - 71: 19.711 distance: 70 - 75: 53.537 distance: 72 - 73: 70.798 distance: 73 - 74: 57.638 distance: 75 - 76: 30.689 distance: 76 - 77: 38.576 distance: 76 - 79: 40.046 distance: 77 - 78: 40.285 distance: 79 - 80: 35.252 distance: 80 - 81: 13.439 distance: 81 - 82: 11.052 distance: 81 - 83: 5.090