Starting phenix.real_space_refine on Fri Sep 27 01:29:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lum_23522/09_2024/7lum_23522.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lum_23522/09_2024/7lum_23522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lum_23522/09_2024/7lum_23522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lum_23522/09_2024/7lum_23522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lum_23522/09_2024/7lum_23522.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lum_23522/09_2024/7lum_23522.cif" } resolution = 4.5 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 394 5.16 5 C 40132 2.51 5 N 11144 2.21 5 O 12308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 516 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63978 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4063 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 18, 'TRANS': 508} Chain: "D" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4063 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 18, 'TRANS': 508} Chain: "M" Number of atoms: 3898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3898 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 9, 'TRANS': 508} Chain: "E" Number of atoms: 3898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3898 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 9, 'TRANS': 508} Chain: "N" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3911 Classifications: {'peptide': 518} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain: "F" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3911 Classifications: {'peptide': 518} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain: "H" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4050 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 16, 'TRANS': 504} Chain: "P" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4050 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 16, 'TRANS': 504} Chain: "K" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4007 Classifications: {'peptide': 522} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 504} Chain: "C" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4007 Classifications: {'peptide': 522} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 504} Chain: "J" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3994 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3994 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "I" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4023 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "A" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4023 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "O" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4043 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "G" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4043 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Time building chain proxies: 25.79, per 1000 atoms: 0.40 Number of scatterers: 63978 At special positions: 0 Unit cell: (191.4, 172.92, 182.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 394 16.00 O 12308 8.00 N 11144 7.00 C 40132 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: 12.39 Conformation dependent library (CDL) restraints added in 6.1 seconds 16684 Ramachandran restraints generated. 8342 Oldfield, 0 Emsley, 8342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15612 Finding SS restraints... Secondary structure from input PDB file: 328 helices and 101 sheets defined 56.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'L' and resid 29 through 50 removed outlier: 3.844A pdb=" N ALA L 33 " --> pdb=" O MET L 29 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR L 50 " --> pdb=" O ASN L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 81 Processing helix chain 'L' and resid 85 through 102 Processing helix chain 'L' and resid 108 through 126 removed outlier: 3.814A pdb=" N ARG L 126 " --> pdb=" O GLN L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 151 removed outlier: 3.551A pdb=" N ILE L 133 " --> pdb=" O HIS L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 173 Processing helix chain 'L' and resid 174 through 180 removed outlier: 6.580A pdb=" N VAL L 177 " --> pdb=" O GLY L 174 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL L 178 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER L 180 " --> pdb=" O VAL L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 197 removed outlier: 3.515A pdb=" N MET L 185 " --> pdb=" O CYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 207 No H-bonds generated for 'chain 'L' and resid 205 through 207' Processing helix chain 'L' and resid 270 through 295 removed outlier: 3.753A pdb=" N LYS L 282 " --> pdb=" O GLN L 278 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE L 285 " --> pdb=" O GLU L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 316 Processing helix chain 'L' and resid 326 through 338 Processing helix chain 'L' and resid 349 through 353 Processing helix chain 'L' and resid 391 through 415 Processing helix chain 'L' and resid 423 through 438 removed outlier: 3.634A pdb=" N ASP L 438 " --> pdb=" O SER L 434 " (cutoff:3.500A) Processing helix chain 'L' and resid 443 through 456 removed outlier: 3.593A pdb=" N ALA L 447 " --> pdb=" O LEU L 443 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 467 removed outlier: 3.707A pdb=" N MET L 460 " --> pdb=" O GLU L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 469 through 484 removed outlier: 3.506A pdb=" N THR L 473 " --> pdb=" O ASN L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 500 through 505 Processing helix chain 'L' and resid 510 through 529 Processing helix chain 'D' and resid 29 through 50 removed outlier: 3.843A pdb=" N ALA D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.813A pdb=" N ARG D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 removed outlier: 3.552A pdb=" N ILE D 133 " --> pdb=" O HIS D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 174 through 180 removed outlier: 6.580A pdb=" N VAL D 177 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL D 178 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 180 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.515A pdb=" N MET D 185 " --> pdb=" O CYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 270 through 295 removed outlier: 3.751A pdb=" N LYS D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 391 through 415 Processing helix chain 'D' and resid 423 through 438 removed outlier: 3.633A pdb=" N ASP D 438 " --> pdb=" O SER D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 456 removed outlier: 3.593A pdb=" N ALA D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 467 removed outlier: 3.707A pdb=" N MET D 460 " --> pdb=" O GLU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 484 removed outlier: 3.506A pdb=" N THR D 473 " --> pdb=" O ASN D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 510 through 529 Processing helix chain 'M' and resid 22 through 40 Processing helix chain 'M' and resid 41 through 43 No H-bonds generated for 'chain 'M' and resid 41 through 43' Processing helix chain 'M' and resid 66 through 74 Processing helix chain 'M' and resid 78 through 95 Processing helix chain 'M' and resid 98 through 120 Processing helix chain 'M' and resid 122 through 144 Processing helix chain 'M' and resid 151 through 168 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.971A pdb=" N HIS M 174 " --> pdb=" O LEU M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 190 Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 208 through 212 Processing helix chain 'M' and resid 260 through 285 removed outlier: 3.595A pdb=" N VAL M 264 " --> pdb=" O SER M 260 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS M 285 " --> pdb=" O ARG M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 307 Processing helix chain 'M' and resid 316 through 328 Processing helix chain 'M' and resid 337 through 341 Processing helix chain 'M' and resid 379 through 403 Processing helix chain 'M' and resid 411 through 427 removed outlier: 3.553A pdb=" N ASN M 426 " --> pdb=" O THR M 422 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG M 427 " --> pdb=" O GLN M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 454 removed outlier: 4.105A pdb=" N VAL M 434 " --> pdb=" O GLY M 430 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA M 435 " --> pdb=" O LYS M 431 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU M 446 " --> pdb=" O ALA M 442 " (cutoff:3.500A) Proline residue: M 447 - end of helix Processing helix chain 'M' and resid 457 through 472 Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'M' and resid 497 through 516 Processing helix chain 'E' and resid 22 through 40 Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 78 through 95 Processing helix chain 'E' and resid 98 through 120 Processing helix chain 'E' and resid 122 through 144 Processing helix chain 'E' and resid 151 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.971A pdb=" N HIS E 174 " --> pdb=" O LEU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 190 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 260 through 285 removed outlier: 3.595A pdb=" N VAL E 264 " --> pdb=" O SER E 260 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 307 Processing helix chain 'E' and resid 316 through 328 Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 379 through 403 Processing helix chain 'E' and resid 411 through 427 removed outlier: 3.553A pdb=" N ASN E 426 " --> pdb=" O THR E 422 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG E 427 " --> pdb=" O GLN E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 454 removed outlier: 4.104A pdb=" N VAL E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 435 " --> pdb=" O LYS E 431 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 446 " --> pdb=" O ALA E 442 " (cutoff:3.500A) Proline residue: E 447 - end of helix Processing helix chain 'E' and resid 457 through 472 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 517 Processing helix chain 'N' and resid 28 through 50 removed outlier: 4.198A pdb=" N THR N 50 " --> pdb=" O ASP N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 81 Processing helix chain 'N' and resid 85 through 102 Processing helix chain 'N' and resid 105 through 126 Processing helix chain 'N' and resid 129 through 152 Processing helix chain 'N' and resid 159 through 172 Processing helix chain 'N' and resid 174 through 178 Processing helix chain 'N' and resid 179 through 195 Proline residue: N 185 - end of helix Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'N' and resid 270 through 293 Processing helix chain 'N' and resid 310 through 321 Processing helix chain 'N' and resid 331 through 341 removed outlier: 4.559A pdb=" N PHE N 335 " --> pdb=" O GLU N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 394 through 418 Processing helix chain 'N' and resid 426 through 443 Processing helix chain 'N' and resid 445 through 459 removed outlier: 3.841A pdb=" N TYR N 449 " --> pdb=" O GLY N 445 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 469 removed outlier: 3.771A pdb=" N SER N 463 " --> pdb=" O GLU N 459 " (cutoff:3.500A) Processing helix chain 'N' and resid 472 through 485 Processing helix chain 'N' and resid 504 through 507 Processing helix chain 'N' and resid 512 through 531 Processing helix chain 'F' and resid 28 through 50 removed outlier: 4.198A pdb=" N THR F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 81 Processing helix chain 'F' and resid 85 through 102 Processing helix chain 'F' and resid 105 through 126 Processing helix chain 'F' and resid 129 through 152 Processing helix chain 'F' and resid 159 through 172 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 179 through 195 Proline residue: F 185 - end of helix Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 270 through 293 Processing helix chain 'F' and resid 310 through 321 Processing helix chain 'F' and resid 331 through 341 removed outlier: 4.560A pdb=" N PHE F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 418 Processing helix chain 'F' and resid 426 through 443 Processing helix chain 'F' and resid 445 through 459 removed outlier: 3.839A pdb=" N TYR F 449 " --> pdb=" O GLY F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.771A pdb=" N SER F 463 " --> pdb=" O GLU F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 504 through 507 Processing helix chain 'F' and resid 512 through 531 Processing helix chain 'H' and resid 19 through 36 Processing helix chain 'H' and resid 37 through 41 removed outlier: 4.113A pdb=" N LEU H 41 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 69 Processing helix chain 'H' and resid 74 through 92 removed outlier: 3.604A pdb=" N LYS H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 111 removed outlier: 3.881A pdb=" N HIS H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 140 removed outlier: 3.838A pdb=" N VAL H 122 " --> pdb=" O HIS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 161 removed outlier: 3.526A pdb=" N MET H 152 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 removed outlier: 4.026A pdb=" N ARG H 167 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 182 Processing helix chain 'H' and resid 185 through 189 removed outlier: 3.760A pdb=" N ASN H 188 " --> pdb=" O PHE H 185 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY H 189 " --> pdb=" O GLU H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 185 through 189' Processing helix chain 'H' and resid 208 through 212 Processing helix chain 'H' and resid 260 through 284 removed outlier: 4.326A pdb=" N PHE H 264 " --> pdb=" O ARG H 260 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 307 Processing helix chain 'H' and resid 316 through 327 Processing helix chain 'H' and resid 334 through 338 Processing helix chain 'H' and resid 339 through 343 Processing helix chain 'H' and resid 380 through 404 Processing helix chain 'H' and resid 412 through 428 Processing helix chain 'H' and resid 433 through 445 removed outlier: 3.777A pdb=" N GLU H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 456 removed outlier: 3.532A pdb=" N ARG H 449 " --> pdb=" O GLU H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 458 through 471 Processing helix chain 'H' and resid 490 through 494 Processing helix chain 'H' and resid 499 through 519 removed outlier: 3.832A pdb=" N ILE H 519 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 36 Processing helix chain 'P' and resid 37 through 41 removed outlier: 4.113A pdb=" N LEU P 41 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 69 Processing helix chain 'P' and resid 74 through 92 removed outlier: 3.604A pdb=" N LYS P 78 " --> pdb=" O HIS P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 111 removed outlier: 3.880A pdb=" N HIS P 111 " --> pdb=" O SER P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 140 removed outlier: 3.837A pdb=" N VAL P 122 " --> pdb=" O HIS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 161 removed outlier: 3.526A pdb=" N MET P 152 " --> pdb=" O ASP P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 167 removed outlier: 4.025A pdb=" N ARG P 167 " --> pdb=" O ALA P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 182 Processing helix chain 'P' and resid 185 through 189 removed outlier: 3.760A pdb=" N ASN P 188 " --> pdb=" O PHE P 185 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY P 189 " --> pdb=" O GLU P 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 185 through 189' Processing helix chain 'P' and resid 208 through 212 Processing helix chain 'P' and resid 260 through 284 removed outlier: 4.326A pdb=" N PHE P 264 " --> pdb=" O ARG P 260 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR P 265 " --> pdb=" O GLU P 261 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU P 272 " --> pdb=" O LEU P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 297 through 307 Processing helix chain 'P' and resid 316 through 327 Processing helix chain 'P' and resid 334 through 338 Processing helix chain 'P' and resid 339 through 343 Processing helix chain 'P' and resid 380 through 404 Processing helix chain 'P' and resid 412 through 428 Processing helix chain 'P' and resid 433 through 445 removed outlier: 3.777A pdb=" N GLU P 445 " --> pdb=" O ALA P 441 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 456 removed outlier: 3.532A pdb=" N ARG P 449 " --> pdb=" O GLU P 445 " (cutoff:3.500A) Processing helix chain 'P' and resid 458 through 471 Processing helix chain 'P' and resid 490 through 494 Processing helix chain 'P' and resid 499 through 519 removed outlier: 3.833A pdb=" N ILE P 519 " --> pdb=" O LEU P 515 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 37 removed outlier: 3.541A pdb=" N VAL K 36 " --> pdb=" O ILE K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 69 Processing helix chain 'K' and resid 73 through 90 removed outlier: 3.520A pdb=" N LYS K 77 " --> pdb=" O HIS K 73 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR K 78 " --> pdb=" O PRO K 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 114 Proline residue: K 110 - end of helix removed outlier: 3.612A pdb=" N GLU K 114 " --> pdb=" O PRO K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 139 removed outlier: 3.928A pdb=" N ILE K 121 " --> pdb=" O HIS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 164 removed outlier: 3.554A pdb=" N SER K 164 " --> pdb=" O MET K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 170 No H-bonds generated for 'chain 'K' and resid 168 through 170' Processing helix chain 'K' and resid 171 through 186 removed outlier: 4.130A pdb=" N LYS K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 208 Processing helix chain 'K' and resid 223 through 227 removed outlier: 4.624A pdb=" N GLU K 226 " --> pdb=" O ALA K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 284 Processing helix chain 'K' and resid 296 through 306 Processing helix chain 'K' and resid 315 through 327 Processing helix chain 'K' and resid 338 through 342 Processing helix chain 'K' and resid 378 through 402 removed outlier: 3.523A pdb=" N GLU K 383 " --> pdb=" O GLU K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 427 removed outlier: 3.640A pdb=" N ARG K 425 " --> pdb=" O ARG K 421 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR K 426 " --> pdb=" O ASP K 422 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE K 427 " --> pdb=" O TYR K 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 443 removed outlier: 4.054A pdb=" N LEU K 433 " --> pdb=" O GLY K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 454 removed outlier: 3.978A pdb=" N ARG K 447 " --> pdb=" O GLU K 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 456 through 471 removed outlier: 4.236A pdb=" N GLN K 470 " --> pdb=" O ALA K 466 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 515 Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.541A pdb=" N VAL C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 73 through 90 removed outlier: 3.521A pdb=" N LYS C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 78 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 114 Proline residue: C 110 - end of helix removed outlier: 3.611A pdb=" N GLU C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 139 removed outlier: 3.927A pdb=" N ILE C 121 " --> pdb=" O HIS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.555A pdb=" N SER C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 186 removed outlier: 4.129A pdb=" N LYS C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 223 through 227 removed outlier: 4.625A pdb=" N GLU C 226 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 284 Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 378 through 402 removed outlier: 3.523A pdb=" N GLU C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 427 removed outlier: 3.641A pdb=" N ARG C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 427 " --> pdb=" O TYR C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 443 removed outlier: 4.054A pdb=" N LEU C 433 " --> pdb=" O GLY C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 454 removed outlier: 3.979A pdb=" N ARG C 447 " --> pdb=" O GLU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 471 removed outlier: 4.236A pdb=" N GLN C 470 " --> pdb=" O ALA C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 515 Processing helix chain 'J' and resid 25 through 30 Processing helix chain 'J' and resid 30 through 43 Processing helix chain 'J' and resid 68 through 75 removed outlier: 3.514A pdb=" N ILE J 72 " --> pdb=" O ASP J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 98 Processing helix chain 'J' and resid 100 through 121 removed outlier: 3.544A pdb=" N GLU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 143 Processing helix chain 'J' and resid 144 through 147 Processing helix chain 'J' and resid 157 through 172 removed outlier: 4.298A pdb=" N THR J 166 " --> pdb=" O SER J 162 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER J 167 " --> pdb=" O LEU J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 190 Processing helix chain 'J' and resid 198 through 202 Processing helix chain 'J' and resid 211 through 215 Processing helix chain 'J' and resid 263 through 286 Processing helix chain 'J' and resid 298 through 308 Processing helix chain 'J' and resid 317 through 329 Processing helix chain 'J' and resid 381 through 405 removed outlier: 3.602A pdb=" N ASP J 405 " --> pdb=" O VAL J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 429 removed outlier: 3.728A pdb=" N THR J 429 " --> pdb=" O SER J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 445 removed outlier: 3.791A pdb=" N PHE J 445 " --> pdb=" O PHE J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 457 Processing helix chain 'J' and resid 459 through 471 removed outlier: 3.574A pdb=" N VAL J 463 " --> pdb=" O LYS J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 474 No H-bonds generated for 'chain 'J' and resid 472 through 474' Processing helix chain 'J' and resid 492 through 496 Processing helix chain 'J' and resid 501 through 521 removed outlier: 3.684A pdb=" N VAL J 521 " --> pdb=" O THR J 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 68 through 75 removed outlier: 3.516A pdb=" N ILE B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 98 Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.543A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 143 Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 157 through 172 removed outlier: 4.298A pdb=" N THR B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 263 through 286 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 317 through 329 Processing helix chain 'B' and resid 381 through 405 removed outlier: 3.602A pdb=" N ASP B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 removed outlier: 3.728A pdb=" N THR B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.792A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 471 removed outlier: 3.574A pdb=" N VAL B 463 " --> pdb=" O LYS B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 501 through 521 removed outlier: 3.683A pdb=" N VAL B 521 " --> pdb=" O THR B 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 35 Processing helix chain 'I' and resid 59 through 67 removed outlier: 3.673A pdb=" N LEU I 63 " --> pdb=" O ASP I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 88 Processing helix chain 'I' and resid 91 through 111 Processing helix chain 'I' and resid 115 through 138 removed outlier: 4.074A pdb=" N ILE I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 157 Processing helix chain 'I' and resid 161 through 178 removed outlier: 3.941A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 282 removed outlier: 3.992A pdb=" N PHE I 266 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE I 267 " --> pdb=" O GLU I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 308 removed outlier: 3.539A pdb=" N GLU I 308 " --> pdb=" O ALA I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 329 Processing helix chain 'I' and resid 340 through 344 Processing helix chain 'I' and resid 380 through 404 Processing helix chain 'I' and resid 412 through 424 Processing helix chain 'I' and resid 431 through 445 removed outlier: 4.003A pdb=" N LEU I 435 " --> pdb=" O GLY I 431 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY I 436 " --> pdb=" O ARG I 432 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU I 445 " --> pdb=" O ALA I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 456 Processing helix chain 'I' and resid 458 through 467 Processing helix chain 'I' and resid 489 through 493 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'A' and resid 15 through 35 Processing helix chain 'A' and resid 59 through 67 removed outlier: 3.674A pdb=" N LEU A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 115 through 138 removed outlier: 4.073A pdb=" N ILE A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.941A pdb=" N GLU A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 282 removed outlier: 3.992A pdb=" N PHE A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.540A pdb=" N GLU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 380 through 404 Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.002A pdb=" N LEU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'O' and resid 14 through 33 removed outlier: 3.584A pdb=" N VAL O 32 " --> pdb=" O ILE O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 65 Processing helix chain 'O' and resid 69 through 86 Processing helix chain 'O' and resid 92 through 109 Processing helix chain 'O' and resid 113 through 134 Processing helix chain 'O' and resid 143 through 157 Processing helix chain 'O' and resid 164 through 179 Processing helix chain 'O' and resid 204 through 208 Processing helix chain 'O' and resid 256 through 258 No H-bonds generated for 'chain 'O' and resid 256 through 258' Processing helix chain 'O' and resid 259 through 281 removed outlier: 3.570A pdb=" N SER O 268 " --> pdb=" O ARG O 264 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR O 271 " --> pdb=" O GLU O 267 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR O 281 " --> pdb=" O LYS O 277 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 304 Processing helix chain 'O' and resid 312 through 324 Processing helix chain 'O' and resid 341 through 345 Processing helix chain 'O' and resid 381 through 405 Processing helix chain 'O' and resid 413 through 431 removed outlier: 4.124A pdb=" N ILE O 421 " --> pdb=" O ALA O 417 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR O 428 " --> pdb=" O GLU O 424 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER O 429 " --> pdb=" O ASN O 425 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET O 430 " --> pdb=" O TYR O 426 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY O 431 " --> pdb=" O ALA O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 433 through 446 removed outlier: 4.047A pdb=" N ALA O 437 " --> pdb=" O ARG O 433 " (cutoff:3.500A) Processing helix chain 'O' and resid 446 through 457 removed outlier: 3.830A pdb=" N ASN O 450 " --> pdb=" O LEU O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 459 through 474 Processing helix chain 'O' and resid 479 through 483 removed outlier: 3.883A pdb=" N ASN O 482 " --> pdb=" O GLU O 479 " (cutoff:3.500A) Processing helix chain 'O' and resid 497 through 502 Processing helix chain 'O' and resid 507 through 526 Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.582A pdb=" N VAL G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'G' and resid 69 through 86 Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 143 through 157 Processing helix chain 'G' and resid 164 through 179 Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 256 through 258 No H-bonds generated for 'chain 'G' and resid 256 through 258' Processing helix chain 'G' and resid 259 through 281 removed outlier: 3.570A pdb=" N SER G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR G 281 " --> pdb=" O LYS G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 304 Processing helix chain 'G' and resid 312 through 324 Processing helix chain 'G' and resid 341 through 345 Processing helix chain 'G' and resid 381 through 405 Processing helix chain 'G' and resid 413 through 431 removed outlier: 4.124A pdb=" N ILE G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER G 429 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET G 430 " --> pdb=" O TYR G 426 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY G 431 " --> pdb=" O ALA G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 446 removed outlier: 4.047A pdb=" N ALA G 437 " --> pdb=" O ARG G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 457 removed outlier: 3.830A pdb=" N ASN G 450 " --> pdb=" O LEU G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 474 Processing helix chain 'G' and resid 479 through 483 removed outlier: 3.882A pdb=" N ASN G 482 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 502 Processing helix chain 'G' and resid 507 through 526 Processing sheet with id=AA1, first strand: chain 'L' and resid 68 through 71 removed outlier: 6.491A pdb=" N ASP L 58 " --> pdb=" O VAL M 517 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN M 519 " --> pdb=" O ASP L 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 209 through 213 removed outlier: 6.570A pdb=" N LYS L 210 " --> pdb=" O ILE L 385 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE L 387 " --> pdb=" O LYS L 210 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU L 212 " --> pdb=" O ILE L 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 228 through 230 removed outlier: 3.684A pdb=" N VAL L 228 " --> pdb=" O ILE L 374 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL L 359 " --> pdb=" O VAL L 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 248 through 251 Processing sheet with id=AA5, first strand: chain 'L' and resid 267 through 268 removed outlier: 3.567A pdb=" N VAL L 268 " --> pdb=" O ARG M 255 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG M 257 " --> pdb=" O VAL L 268 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL M 256 " --> pdb=" O GLN N 263 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL N 265 " --> pdb=" O VAL M 256 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL M 258 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE N 264 " --> pdb=" O GLN O 251 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL O 253 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL N 266 " --> pdb=" O VAL O 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'L' and resid 530 through 534 removed outlier: 5.271A pdb=" N ILE L 530 " --> pdb=" O ASP K 46 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU K 48 " --> pdb=" O ILE L 530 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP L 532 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 68 through 71 Processing sheet with id=AA9, first strand: chain 'D' and resid 209 through 213 removed outlier: 6.569A pdb=" N LYS D 210 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE D 387 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU D 212 " --> pdb=" O ILE D 387 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 228 through 230 removed outlier: 3.683A pdb=" N VAL D 228 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 359 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB3, first strand: chain 'D' and resid 267 through 268 removed outlier: 3.591A pdb=" N VAL D 268 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 257 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 256 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL F 265 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL E 258 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE F 264 " --> pdb=" O GLN G 251 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL G 253 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL F 266 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'D' and resid 530 through 534 removed outlier: 5.279A pdb=" N ILE D 530 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU C 48 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP D 532 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 61 through 64 removed outlier: 7.152A pdb=" N ASP M 49 " --> pdb=" O ASP N 534 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N VAL N 536 " --> pdb=" O ASP M 49 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE M 51 " --> pdb=" O VAL N 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 146 through 147 Processing sheet with id=AB8, first strand: chain 'M' and resid 199 through 203 Processing sheet with id=AB9, first strand: chain 'M' and resid 218 through 220 removed outlier: 6.695A pdb=" N VAL M 365 " --> pdb=" O CYS M 346 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS M 346 " --> pdb=" O VAL M 365 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 218 through 220 removed outlier: 6.695A pdb=" N VAL M 365 " --> pdb=" O CYS M 346 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS M 346 " --> pdb=" O VAL M 365 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS M 236 " --> pdb=" O CYS M 289 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE M 291 " --> pdb=" O LYS M 236 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU M 238 " --> pdb=" O ILE M 291 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE M 290 " --> pdb=" O ILE M 312 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 476 through 479 removed outlier: 3.509A pdb=" N THR M 484 " --> pdb=" O ASP M 479 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 61 through 64 removed outlier: 7.402A pdb=" N ASP E 49 " --> pdb=" O ASP F 534 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N VAL F 536 " --> pdb=" O ASP E 49 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE E 51 " --> pdb=" O VAL F 536 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC5, first strand: chain 'E' and resid 199 through 203 Processing sheet with id=AC6, first strand: chain 'E' and resid 218 through 220 removed outlier: 6.694A pdb=" N VAL E 365 " --> pdb=" O CYS E 346 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS E 346 " --> pdb=" O VAL E 365 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 218 through 220 removed outlier: 6.694A pdb=" N VAL E 365 " --> pdb=" O CYS E 346 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS E 346 " --> pdb=" O VAL E 365 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS E 236 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE E 291 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 238 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE E 290 " --> pdb=" O ILE E 312 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 476 through 479 removed outlier: 3.510A pdb=" N THR E 484 " --> pdb=" O ASP E 479 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 68 through 71 Processing sheet with id=AD1, first strand: chain 'N' and resid 153 through 154 Processing sheet with id=AD2, first strand: chain 'N' and resid 208 through 212 removed outlier: 3.833A pdb=" N THR N 387 " --> pdb=" O VAL N 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL N 224 " --> pdb=" O THR N 387 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 226 through 229 removed outlier: 3.613A pdb=" N ALA N 362 " --> pdb=" O VAL N 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 323 through 328 removed outlier: 3.753A pdb=" N GLN N 301 " --> pdb=" O ILE N 249 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 491 through 493 Processing sheet with id=AD6, first strand: chain 'F' and resid 68 through 71 Processing sheet with id=AD7, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AD8, first strand: chain 'F' and resid 208 through 212 removed outlier: 3.834A pdb=" N THR F 387 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL F 224 " --> pdb=" O THR F 387 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 226 through 229 removed outlier: 3.614A pdb=" N ALA F 362 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 323 through 328 removed outlier: 3.753A pdb=" N GLN F 301 " --> pdb=" O ILE F 249 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 491 through 493 Processing sheet with id=AE3, first strand: chain 'H' and resid 16 through 18 Processing sheet with id=AE4, first strand: chain 'H' and resid 57 through 59 removed outlier: 7.872A pdb=" N MET H 49 " --> pdb=" O MET A 522 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 142 through 143 Processing sheet with id=AE6, first strand: chain 'H' and resid 199 through 204 removed outlier: 6.610A pdb=" N ARG H 200 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU H 376 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU H 202 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR H 373 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 215 " --> pdb=" O THR H 373 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 218 through 220 removed outlier: 3.628A pdb=" N VAL H 218 " --> pdb=" O ILE H 363 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE H 363 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 238 through 241 removed outlier: 6.248A pdb=" N VAL H 290 " --> pdb=" O ILE H 312 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=AF1, first strand: chain 'P' and resid 16 through 18 Processing sheet with id=AF2, first strand: chain 'P' and resid 57 through 59 removed outlier: 4.369A pdb=" N MET I 522 " --> pdb=" O MET P 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 142 through 143 Processing sheet with id=AF4, first strand: chain 'P' and resid 199 through 204 removed outlier: 6.610A pdb=" N ARG P 200 " --> pdb=" O ILE P 374 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU P 376 " --> pdb=" O ARG P 200 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU P 202 " --> pdb=" O LEU P 376 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR P 373 " --> pdb=" O LEU P 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU P 215 " --> pdb=" O THR P 373 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 218 through 220 removed outlier: 3.629A pdb=" N VAL P 218 " --> pdb=" O ILE P 363 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE P 363 " --> pdb=" O VAL P 218 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 238 through 241 removed outlier: 6.248A pdb=" N VAL P 290 " --> pdb=" O ILE P 312 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 478 through 480 Processing sheet with id=AF8, first strand: chain 'K' and resid 15 through 17 removed outlier: 3.750A pdb=" N SER K 16 " --> pdb=" O THR K 519 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR K 519 " --> pdb=" O SER K 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'K' and resid 196 through 198 Processing sheet with id=AG1, first strand: chain 'K' and resid 213 through 216 removed outlier: 3.553A pdb=" N ASN K 359 " --> pdb=" O PHE K 216 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 309 through 310 Processing sheet with id=AG3, first strand: chain 'K' and resid 352 through 353 Processing sheet with id=AG4, first strand: chain 'K' and resid 405 through 407 Processing sheet with id=AG5, first strand: chain 'K' and resid 475 through 478 Processing sheet with id=AG6, first strand: chain 'C' and resid 15 through 17 removed outlier: 3.750A pdb=" N SER C 16 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 519 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU C 518 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE B 57 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 520 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 196 through 198 Processing sheet with id=AG8, first strand: chain 'C' and resid 213 through 216 removed outlier: 3.553A pdb=" N ASN C 359 " --> pdb=" O PHE C 216 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AH1, first strand: chain 'C' and resid 253 through 255 removed outlier: 7.280A pdb=" N GLU C 254 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 250 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 352 through 353 Processing sheet with id=AH3, first strand: chain 'C' and resid 405 through 407 Processing sheet with id=AH4, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AH5, first strand: chain 'J' and resid 19 through 21 removed outlier: 3.658A pdb=" N ILE J 525 " --> pdb=" O MET I 46 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 54 through 57 Processing sheet with id=AH7, first strand: chain 'J' and resid 203 through 208 removed outlier: 3.735A pdb=" N GLY J 379 " --> pdb=" O ILE J 207 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 221 through 223 Processing sheet with id=AH9, first strand: chain 'J' and resid 239 through 242 removed outlier: 6.570A pdb=" N ALA J 240 " --> pdb=" O VAL J 292 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 256 through 257 removed outlier: 6.619A pdb=" N THR J 256 " --> pdb=" O TYR I 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'J' and resid 408 through 410 Processing sheet with id=AI3, first strand: chain 'J' and resid 478 through 479 Processing sheet with id=AI4, first strand: chain 'B' and resid 19 through 21 removed outlier: 3.888A pdb=" N VAL A 48 " --> pdb=" O ILE B 525 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 527 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'B' and resid 203 through 208 removed outlier: 3.736A pdb=" N GLY B 379 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AI7, first strand: chain 'B' and resid 239 through 242 removed outlier: 6.569A pdb=" N ALA B 240 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=AI9, first strand: chain 'B' and resid 478 through 479 Processing sheet with id=AJ1, first strand: chain 'I' and resid 139 through 140 Processing sheet with id=AJ2, first strand: chain 'I' and resid 191 through 196 removed outlier: 6.834A pdb=" N GLU I 192 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE I 376 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET I 194 " --> pdb=" O ILE I 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR I 373 " --> pdb=" O ILE I 207 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU I 375 " --> pdb=" O SER I 205 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 211 through 212 Processing sheet with id=AJ4, first strand: chain 'I' and resid 311 through 314 removed outlier: 5.911A pdb=" N TYR I 229 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE I 292 " --> pdb=" O TYR I 229 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU I 231 " --> pdb=" O ILE I 292 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'I' and resid 477 through 479 Processing sheet with id=AJ6, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AJ7, first strand: chain 'A' and resid 191 through 196 removed outlier: 6.834A pdb=" N GLU A 192 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 376 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET A 194 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 373 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 375 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AJ9, first strand: chain 'A' and resid 311 through 314 removed outlier: 5.912A pdb=" N TYR A 229 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE A 292 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 231 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'A' and resid 477 through 479 Processing sheet with id=AK2, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AK3, first strand: chain 'O' and resid 196 through 201 removed outlier: 6.126A pdb=" N ASN O 196 " --> pdb=" O ILE O 375 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU O 377 " --> pdb=" O ASN O 196 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU O 198 " --> pdb=" O LEU O 377 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLY O 379 " --> pdb=" O LEU O 198 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA O 200 " --> pdb=" O GLY O 379 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 213 through 216 removed outlier: 3.607A pdb=" N GLU O 350 " --> pdb=" O LYS O 365 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'O' and resid 234 through 236 Processing sheet with id=AK6, first strand: chain 'O' and resid 408 through 410 Processing sheet with id=AK7, first strand: chain 'G' and resid 43 through 45 Processing sheet with id=AK8, first strand: chain 'G' and resid 196 through 201 removed outlier: 6.125A pdb=" N ASN G 196 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU G 377 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU G 198 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLY G 379 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA G 200 " --> pdb=" O GLY G 379 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 213 through 216 removed outlier: 3.608A pdb=" N GLU G 350 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 234 through 236 Processing sheet with id=AL2, first strand: chain 'G' and resid 408 through 410 3787 hydrogen bonds defined for protein. 10854 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: 29.71 Time building geometry restraints manager: 14.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 21545 1.34 - 1.46: 9339 1.46 - 1.58: 33178 1.58 - 1.70: 0 1.70 - 1.82: 652 Bond restraints: 64714 Sorted by residual: bond pdb=" C LEU I 517 " pdb=" N VAL I 518 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.56e-02 4.11e+03 5.74e+00 bond pdb=" C LEU A 517 " pdb=" N VAL A 518 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.56e-02 4.11e+03 5.39e+00 bond pdb=" CB ARG O 266 " pdb=" CG ARG O 266 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.39e+00 bond pdb=" C LYS P 286 " pdb=" O LYS P 286 " ideal model delta sigma weight residual 1.235 1.245 -0.010 4.70e-03 4.53e+04 4.28e+00 bond pdb=" CB ARG G 266 " pdb=" CG ARG G 266 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.25e+00 ... (remaining 64709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 86317 3.12 - 6.24: 891 6.24 - 9.36: 96 9.36 - 12.49: 6 12.49 - 15.61: 2 Bond angle restraints: 87312 Sorted by residual: angle pdb=" C ARG J 404 " pdb=" N ASP J 405 " pdb=" CA ASP J 405 " ideal model delta sigma weight residual 121.90 115.14 6.76 1.26e+00 6.30e-01 2.88e+01 angle pdb=" C ARG B 404 " pdb=" N ASP B 405 " pdb=" CA ASP B 405 " ideal model delta sigma weight residual 121.90 115.15 6.75 1.26e+00 6.30e-01 2.87e+01 angle pdb=" CB MET H 46 " pdb=" CG MET H 46 " pdb=" SD MET H 46 " ideal model delta sigma weight residual 112.70 97.09 15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" CB MET P 46 " pdb=" CG MET P 46 " pdb=" SD MET P 46 " ideal model delta sigma weight residual 112.70 97.10 15.60 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C THR L 162 " pdb=" N GLU L 163 " pdb=" CA GLU L 163 " ideal model delta sigma weight residual 121.80 109.38 12.42 2.44e+00 1.68e-01 2.59e+01 ... (remaining 87307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 36498 18.06 - 36.13: 3044 36.13 - 54.19: 464 54.19 - 72.26: 106 72.26 - 90.32: 70 Dihedral angle restraints: 40182 sinusoidal: 16080 harmonic: 24102 Sorted by residual: dihedral pdb=" CA CYS L 440 " pdb=" C CYS L 440 " pdb=" N PRO L 441 " pdb=" CA PRO L 441 " ideal model delta harmonic sigma weight residual -180.00 -123.60 -56.40 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA CYS D 440 " pdb=" C CYS D 440 " pdb=" N PRO D 441 " pdb=" CA PRO D 441 " ideal model delta harmonic sigma weight residual -180.00 -123.70 -56.30 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA PRO D 441 " pdb=" C PRO D 441 " pdb=" N THR D 442 " pdb=" CA THR D 442 " ideal model delta harmonic sigma weight residual -180.00 -126.83 -53.17 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 40179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 7361 0.044 - 0.087: 2261 0.087 - 0.131: 750 0.131 - 0.174: 63 0.174 - 0.218: 21 Chirality restraints: 10456 Sorted by residual: chirality pdb=" CA PRO L 441 " pdb=" N PRO L 441 " pdb=" C PRO L 441 " pdb=" CB PRO L 441 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA PRO D 441 " pdb=" N PRO D 441 " pdb=" C PRO D 441 " pdb=" CB PRO D 441 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU F 512 " pdb=" CB LEU F 512 " pdb=" CD1 LEU F 512 " pdb=" CD2 LEU F 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 10453 not shown) Planarity restraints: 11218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 163 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C GLU L 163 " -0.069 2.00e-02 2.50e+03 pdb=" O GLU L 163 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO L 164 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 163 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLU D 163 " -0.069 2.00e-02 2.50e+03 pdb=" O GLU D 163 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO D 164 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 430 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 431 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 431 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 431 " 0.049 5.00e-02 4.00e+02 ... (remaining 11215 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 1049 2.56 - 3.14: 61017 3.14 - 3.73: 106830 3.73 - 4.31: 140277 4.31 - 4.90: 220872 Nonbonded interactions: 530045 Sorted by model distance: nonbonded pdb=" OD1 ASN P 28 " pdb=" OH TYR B 30 " model vdw 1.970 3.040 nonbonded pdb=" OD1 ASP J 522 " pdb=" NZ LYS I 45 " model vdw 1.972 3.120 nonbonded pdb=" OD1 ASP B 522 " pdb=" NZ LYS A 45 " model vdw 2.018 3.120 nonbonded pdb=" OG1 THR M 42 " pdb=" OD1 ASN M 65 " model vdw 2.065 3.040 nonbonded pdb=" OG1 THR E 42 " pdb=" OD1 ASN E 65 " model vdw 2.065 3.040 ... (remaining 530040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } Set up NCS constraints Number of NCS constrained groups: 8 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'P' } 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: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.780 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 114.600 Find NCS groups from input model: 4.500 Set up NCS constraints: 0.360 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.007 0.071 64714 Z= 0.429 Angle : 0.849 15.607 87312 Z= 0.469 Chirality : 0.047 0.218 10456 Planarity : 0.005 0.091 11218 Dihedral : 14.021 90.321 24570 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.50 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 3.51 % Twisted General : 0.17 % 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: -0.70 (0.09), residues: 8342 helix: 0.48 (0.08), residues: 4222 sheet: -1.23 (0.16), residues: 1014 loop : -1.41 (0.11), residues: 3106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP O 485 HIS 0.018 0.002 HIS D 37 PHE 0.039 0.002 PHE C 381 TYR 0.023 0.002 TYR A 498 ARG 0.014 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16684 Ramachandran restraints generated. 8342 Oldfield, 0 Emsley, 8342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16684 Ramachandran restraints generated. 8342 Oldfield, 0 Emsley, 8342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8974 (tp) cc_final: 0.8675 (tp) REVERT: A 167 VAL cc_start: 0.9127 (t) cc_final: 0.8743 (p) REVERT: A 190 MET cc_start: 0.6642 (pmm) cc_final: 0.5523 (pmm) REVERT: A 408 VAL cc_start: 0.8524 (t) cc_final: 0.8077 (p) REVERT: A 504 LEU cc_start: 0.8485 (pp) cc_final: 0.8263 (tt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1259 time to fit residues: 24.5685 Evaluate side-chains 94 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.346 Evaluate side-chains 138 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8069 (tt0) REVERT: B 103 PHE cc_start: 0.7192 (m-10) cc_final: 0.6892 (m-80) REVERT: B 113 GLU cc_start: 0.8623 (tp30) cc_final: 0.8251 (mm-30) REVERT: B 169 MET cc_start: 0.7017 (tmm) cc_final: 0.6190 (tmm) REVERT: B 327 THR cc_start: 0.7526 (p) cc_final: 0.5895 (p) REVERT: B 352 LEU cc_start: 0.7729 (tp) cc_final: 0.7478 (tt) REVERT: B 383 ASN cc_start: 0.8968 (m-40) cc_final: 0.8197 (p0) REVERT: B 385 MET cc_start: 0.8235 (mmt) cc_final: 0.7817 (mmm) REVERT: B 521 VAL cc_start: 0.8826 (t) cc_final: 0.8595 (m) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1066 time to fit residues: 18.8720 Evaluate side-chains 89 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.337 Evaluate side-chains 149 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 LYS cc_start: 0.8820 (mttp) cc_final: 0.8571 (ttmm) REVERT: C 98 THR cc_start: 0.9653 (m) cc_final: 0.9430 (p) REVERT: C 122 ILE cc_start: 0.9455 (pt) cc_final: 0.9111 (mt) REVERT: C 262 ASP cc_start: 0.8648 (m-30) cc_final: 0.8261 (m-30) REVERT: C 326 CYS cc_start: 0.7000 (m) cc_final: 0.6790 (m) REVERT: C 380 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8268 (mm-40) REVERT: C 512 LEU cc_start: 0.9124 (tp) cc_final: 0.8830 (tp) REVERT: C 516 VAL cc_start: 0.9161 (t) cc_final: 0.8827 (t) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1141 time to fit residues: 21.4740 Evaluate side-chains 86 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.344 Evaluate side-chains 146 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 23 ASP cc_start: 0.8554 (p0) cc_final: 0.8158 (p0) REVERT: D 50 THR cc_start: 0.8767 (p) cc_final: 0.8559 (t) REVERT: D 52 LEU cc_start: 0.8487 (tp) cc_final: 0.8190 (tp) REVERT: D 58 ASP cc_start: 0.7052 (p0) cc_final: 0.6569 (p0) REVERT: D 91 MET cc_start: 0.9022 (mmp) cc_final: 0.8806 (mmp) REVERT: D 267 ASP cc_start: 0.5166 (p0) cc_final: 0.4767 (p0) REVERT: D 333 ILE cc_start: 0.9238 (mm) cc_final: 0.9021 (mm) REVERT: D 429 CYS cc_start: 0.9107 (m) cc_final: 0.8810 (t) REVERT: D 481 GLN cc_start: 0.8511 (tt0) cc_final: 0.7645 (tp40) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1161 time to fit residues: 21.3773 Evaluate side-chains 90 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.353 Evaluate side-chains 152 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: E 48 MET cc_start: 0.8432 (mmt) cc_final: 0.7654 (ttt) REVERT: E 127 ILE cc_start: 0.8592 (mm) cc_final: 0.7951 (mm) REVERT: E 134 THR cc_start: 0.9306 (m) cc_final: 0.9088 (p) REVERT: E 141 LEU cc_start: 0.9326 (tp) cc_final: 0.8819 (mm) REVERT: E 179 PHE cc_start: 0.8375 (m-80) cc_final: 0.8130 (m-10) REVERT: E 267 ILE cc_start: 0.9152 (mm) cc_final: 0.8605 (mm) REVERT: E 271 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7777 (mt-10) REVERT: E 275 MET cc_start: 0.7999 (tpt) cc_final: 0.7276 (tpp) REVERT: E 356 GLU cc_start: 0.7758 (pp20) cc_final: 0.7356 (mp0) REVERT: E 384 ASP cc_start: 0.7400 (t70) cc_final: 0.7192 (t0) REVERT: E 414 GLU cc_start: 0.8778 (mp0) cc_final: 0.8136 (mm-30) REVERT: E 417 MET cc_start: 0.7148 (mtt) cc_final: 0.5768 (mtt) REVERT: E 456 TYR cc_start: 0.6942 (m-80) cc_final: 0.6738 (m-80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1126 time to fit residues: 21.5300 Evaluate side-chains 91 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.329 Evaluate side-chains 136 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 33 ILE cc_start: 0.8258 (mt) cc_final: 0.7495 (mt) REVERT: F 57 MET cc_start: 0.7920 (mmt) cc_final: 0.7271 (tpt) REVERT: F 133 ILE cc_start: 0.9303 (mm) cc_final: 0.9026 (mm) REVERT: F 155 VAL cc_start: 0.8095 (t) cc_final: 0.7895 (p) REVERT: F 179 TYR cc_start: 0.7123 (m-80) cc_final: 0.6827 (m-10) REVERT: F 283 ILE cc_start: 0.8253 (mm) cc_final: 0.7793 (tt) REVERT: F 407 ASP cc_start: 0.7026 (m-30) cc_final: 0.6810 (t0) REVERT: F 537 ASN cc_start: 0.8542 (m-40) cc_final: 0.8064 (t0) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1097 time to fit residues: 18.9405 Evaluate side-chains 84 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.335 Evaluate side-chains 142 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 PHE cc_start: 0.7405 (m-80) cc_final: 0.7129 (m-80) REVERT: G 115 THR cc_start: 0.8992 (m) cc_final: 0.8733 (m) REVERT: G 147 CYS cc_start: 0.9364 (m) cc_final: 0.9041 (p) REVERT: G 297 LEU cc_start: 0.8960 (mt) cc_final: 0.8645 (mt) REVERT: G 388 MET cc_start: 0.8863 (ptp) cc_final: 0.8599 (ptm) REVERT: G 389 GLU cc_start: 0.7823 (pp20) cc_final: 0.7471 (pp20) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1271 time to fit residues: 22.4640 Evaluate side-chains 80 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.347 Evaluate side-chains 157 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 22 VAL cc_start: 0.9147 (t) cc_final: 0.7095 (t) REVERT: H 36 ILE cc_start: 0.8631 (pt) cc_final: 0.8414 (tt) REVERT: H 47 MET cc_start: 0.7861 (tpp) cc_final: 0.7239 (pmm) REVERT: H 133 MET cc_start: 0.9053 (mtm) cc_final: 0.8638 (mtp) REVERT: H 203 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7651 (mttp) REVERT: H 281 ASP cc_start: 0.8484 (m-30) cc_final: 0.7668 (t0) REVERT: H 301 GLN cc_start: 0.8758 (tt0) cc_final: 0.8505 (tm-30) REVERT: H 310 THR cc_start: 0.8427 (m) cc_final: 0.8096 (p) REVERT: H 350 LEU cc_start: 0.8832 (tp) cc_final: 0.8615 (mm) REVERT: H 364 THR cc_start: 0.8075 (p) cc_final: 0.7772 (t) REVERT: H 388 GLU cc_start: 0.7993 (pp20) cc_final: 0.7135 (pp20) REVERT: H 416 MET cc_start: 0.7707 (mmp) cc_final: 0.7317 (mmm) REVERT: H 450 THR cc_start: 0.8856 (p) cc_final: 0.8526 (t) REVERT: H 460 ILE cc_start: 0.8497 (tp) cc_final: 0.8252 (mp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1206 time to fit residues: 24.3494 Evaluate side-chains 99 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 700 optimal weight: 0.0270 chunk 629 optimal weight: 2.9990 chunk 349 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 424 optimal weight: 4.9990 chunk 336 optimal weight: 0.2980 chunk 650 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 395 optimal weight: 2.9990 chunk 484 optimal weight: 8.9990 chunk 753 optimal weight: 5.9990 overall best weight: 1.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 218 HIS A 386 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 41 GLN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 461 ASN 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: K 258 HIS 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: ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 GLN D 515 GLN 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: M 228 GLN M 361 HIS 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: N 138 GLN N 262 ASN 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: G 103 ASN G 113 HIS ** G 353 GLN ** 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: P 61 ASN ** P 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 64714 Z= 0.265 Angle : 0.796 25.080 87312 Z= 0.412 Chirality : 0.048 0.288 10456 Planarity : 0.005 0.088 11218 Dihedral : 6.196 56.593 8892 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 0.43 % Allowed : 5.35 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 3.51 % Twisted General : 0.15 % 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: -0.36 (0.09), residues: 8342 helix: 0.74 (0.08), residues: 4312 sheet: -0.98 (0.15), residues: 1110 loop : -1.34 (0.12), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 485 HIS 0.012 0.002 HIS D 312 PHE 0.058 0.003 PHE I 249 TYR 0.030 0.002 TYR L 280 ARG 0.025 0.001 ARG L 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.6206 (tp) cc_final: 0.5617 (tt) REVERT: A 167 VAL cc_start: 0.9123 (t) cc_final: 0.8697 (p) REVERT: A 194 MET cc_start: 0.7658 (pmm) cc_final: 0.7226 (pmm) REVERT: A 202 THR cc_start: 0.8693 (p) cc_final: 0.8254 (t) REVERT: A 245 ASN cc_start: 0.7813 (p0) cc_final: 0.7554 (p0) REVERT: A 408 VAL cc_start: 0.9254 (t) cc_final: 0.8830 (p) outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.1095 time to fit residues: 17.2804 Evaluate side-chains 92 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.351 Evaluate side-chains 120 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: J 14 MET cc_start: 0.8385 (mpp) cc_final: 0.8112 (mmm) REVERT: J 22 PHE cc_start: 0.8477 (m-80) cc_final: 0.8249 (m-10) REVERT: J 31 ARG cc_start: 0.7109 (tpp80) cc_final: 0.6652 (mmm160) REVERT: J 116 GLU cc_start: 0.8951 (pp20) cc_final: 0.8714 (tm-30) REVERT: J 259 ILE cc_start: 0.8215 (pt) cc_final: 0.7339 (pt) REVERT: J 311 MET cc_start: 0.7838 (mmp) cc_final: 0.7577 (mmt) REVERT: J 385 MET cc_start: 0.8976 (mmt) cc_final: 0.8440 (mmp) outliers start: 2 outliers final: 0 residues processed: 120 average time/residue: 0.1208 time to fit residues: 18.2674 Evaluate side-chains 75 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.347 Evaluate side-chains 158 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 9 LEU cc_start: 0.5860 (mm) cc_final: 0.5481 (mt) REVERT: K 73 HIS cc_start: 0.8479 (t-90) cc_final: 0.6534 (m90) REVERT: K 192 LEU cc_start: 0.8655 (mp) cc_final: 0.8294 (mt) REVERT: K 240 LEU cc_start: 0.9469 (mm) cc_final: 0.9219 (mp) REVERT: K 361 PHE cc_start: 0.6232 (p90) cc_final: 0.5557 (p90) REVERT: K 380 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8554 (mm110) REVERT: K 394 MET cc_start: 0.8235 (tmm) cc_final: 0.8019 (tmm) REVERT: K 497 MET cc_start: 0.8046 (mmp) cc_final: 0.6853 (mmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1419 time to fit residues: 27.2093 Evaluate side-chains 101 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.338 Evaluate side-chains 112 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 ASP cc_start: 0.8389 (p0) cc_final: 0.8031 (p0) REVERT: D 50 THR cc_start: 0.9141 (p) cc_final: 0.8886 (t) REVERT: D 52 LEU cc_start: 0.8606 (tp) cc_final: 0.8384 (tp) REVERT: D 58 ASP cc_start: 0.7265 (p0) cc_final: 0.6924 (p0) REVERT: D 91 MET cc_start: 0.9071 (mmp) cc_final: 0.8631 (mmp) REVERT: D 133 ILE cc_start: 0.9711 (mt) cc_final: 0.9383 (tt) REVERT: D 196 VAL cc_start: 0.8961 (t) cc_final: 0.8618 (p) REVERT: D 198 ASP cc_start: 0.7840 (t0) cc_final: 0.7582 (t0) REVERT: D 265 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5666 (tptp) REVERT: D 267 ASP cc_start: 0.4848 (p0) cc_final: 0.4271 (p0) REVERT: D 333 ILE cc_start: 0.9257 (mm) cc_final: 0.9048 (mm) REVERT: D 429 CYS cc_start: 0.9059 (m) cc_final: 0.8770 (t) REVERT: D 480 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7627 (mmm-85) REVERT: D 527 ILE cc_start: 0.9356 (mm) cc_final: 0.9137 (tp) outliers start: 4 outliers final: 0 residues processed: 109 average time/residue: 0.1080 time to fit residues: 15.2805 Evaluate side-chains 88 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.349 Evaluate side-chains 119 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: M 37 ASP cc_start: 0.7848 (m-30) cc_final: 0.7507 (m-30) REVERT: M 134 THR cc_start: 0.9135 (m) cc_final: 0.8730 (p) REVERT: M 218 PHE cc_start: 0.7303 (t80) cc_final: 0.6986 (t80) REVERT: M 222 LYS cc_start: 0.8779 (mppt) cc_final: 0.8564 (mtmt) REVERT: M 263 LYS cc_start: 0.8094 (mttt) cc_final: 0.7853 (mmtt) REVERT: M 279 VAL cc_start: 0.9103 (t) cc_final: 0.8870 (t) REVERT: M 287 ILE cc_start: 0.8617 (mm) cc_final: 0.8381 (mm) REVERT: M 381 GLN cc_start: 0.9126 (mp10) cc_final: 0.8777 (mp10) REVERT: M 424 LEU cc_start: 0.8800 (tp) cc_final: 0.8310 (tp) REVERT: M 449 ILE cc_start: 0.9420 (mm) cc_final: 0.9118 (tt) REVERT: M 465 LEU cc_start: 0.8826 (tp) cc_final: 0.7977 (tp) REVERT: M 516 ARG cc_start: 0.7019 (mmm-85) cc_final: 0.6647 (tpt170) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.1164 time to fit residues: 17.4648 Evaluate side-chains 84 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.327 Evaluate side-chains 140 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 186 MET cc_start: 0.8691 (mmt) cc_final: 0.8170 (mmm) REVERT: N 271 GLN cc_start: 0.7766 (mt0) cc_final: 0.7199 (mp10) REVERT: N 460 VAL cc_start: 0.8946 (t) cc_final: 0.8585 (m) outliers start: 4 outliers final: 0 residues processed: 139 average time/residue: 0.1234 time to fit residues: 21.3016 Evaluate side-chains 78 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.336 Evaluate side-chains 109 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 147 CYS cc_start: 0.9306 (m) cc_final: 0.9017 (p) REVERT: G 160 ILE cc_start: 0.8814 (mm) cc_final: 0.8124 (mm) REVERT: G 281 THR cc_start: 0.7208 (m) cc_final: 0.6742 (m) REVERT: G 297 LEU cc_start: 0.9115 (mt) cc_final: 0.8796 (mt) REVERT: G 377 LEU cc_start: 0.9087 (mm) cc_final: 0.8734 (mm) REVERT: G 387 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8225 (pp20) REVERT: G 388 MET cc_start: 0.8982 (ptp) cc_final: 0.8676 (ptm) REVERT: G 389 GLU cc_start: 0.8038 (pp20) cc_final: 0.7579 (pp20) REVERT: G 430 MET cc_start: 0.7573 (tpt) cc_final: 0.7186 (tpp) REVERT: G 530 LEU cc_start: 0.9167 (mm) cc_final: 0.8939 (mm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0878 time to fit residues: 13.0184 Evaluate side-chains 78 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.345 Evaluate side-chains 171 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 50 LEU cc_start: 0.9328 (mm) cc_final: 0.8802 (mm) REVERT: P 51 LEU cc_start: 0.8557 (mt) cc_final: 0.7965 (pt) REVERT: P 80 MET cc_start: 0.9270 (mmm) cc_final: 0.8573 (tpp) REVERT: P 99 ILE cc_start: 0.9365 (pt) cc_final: 0.9156 (pt) REVERT: P 120 THR cc_start: 0.9346 (p) cc_final: 0.8807 (p) REVERT: P 130 LEU cc_start: 0.9087 (tp) cc_final: 0.8577 (tp) REVERT: P 132 ASP cc_start: 0.8457 (m-30) cc_final: 0.8219 (m-30) REVERT: P 133 MET cc_start: 0.8968 (mtm) cc_final: 0.8492 (mtt) REVERT: P 173 CYS cc_start: 0.8759 (p) cc_final: 0.8077 (m) REVERT: P 180 VAL cc_start: 0.9170 (p) cc_final: 0.8922 (p) REVERT: P 247 TYR cc_start: 0.5874 (p90) cc_final: 0.5607 (p90) REVERT: P 263 ASP cc_start: 0.8353 (m-30) cc_final: 0.7781 (m-30) REVERT: P 289 VAL cc_start: 0.8605 (t) cc_final: 0.8120 (t) REVERT: P 416 MET cc_start: 0.7308 (mmp) cc_final: 0.7089 (mmp) REVERT: P 498 PRO cc_start: 0.8537 (Cg_exo) cc_final: 0.7911 (Cg_endo) REVERT: P 519 ILE cc_start: 0.9437 (mm) cc_final: 0.9077 (tp) REVERT: P 527 LYS cc_start: 0.9327 (mttt) cc_final: 0.8736 (mmtt) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.1271 time to fit residues: 26.8554 Evaluate side-chains 108 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 418 optimal weight: 40.0000 chunk 233 optimal weight: 20.0000 chunk 627 optimal weight: 2.9990 chunk 513 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 755 optimal weight: 9.9990 chunk 815 optimal weight: 9.9990 chunk 672 optimal weight: 4.9990 chunk 748 optimal weight: 0.0970 chunk 257 optimal weight: 5.9990 chunk 605 optimal weight: 10.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 HIS ** 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: J 21 HIS ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 HIS J 397 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 459 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: D 37 HIS D 55 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** 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: M 178 HIS M 361 HIS ** M 399 GLN ** 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: N 72 ASN ** N 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 GLN N 262 ASN N 289 GLN N 350 GLN Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 333 ASN ** G 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: P 61 ASN P 74 HIS P 284 GLN ** P 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.229 64714 Z= 0.481 Angle : 1.168 40.299 87312 Z= 0.602 Chirality : 0.065 1.015 10456 Planarity : 0.011 0.320 11218 Dihedral : 6.468 49.942 8892 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.23 % Favored : 93.55 % Rotamer: Outliers : 0.74 % Allowed : 5.29 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 3.51 % Twisted General : 0.15 % 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: -1.40 (0.09), residues: 8342 helix: -0.26 (0.07), residues: 4306 sheet: -1.27 (0.15), residues: 1122 loop : -1.63 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP D 324 HIS 0.069 0.004 HIS D 495 PHE 0.108 0.006 PHE D 345 TYR 0.108 0.004 TYR L 446 ARG 0.128 0.003 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.6023 (tp) cc_final: 0.5463 (tt) REVERT: A 123 PHE cc_start: 0.8645 (m-10) cc_final: 0.8256 (m-80) REVERT: A 167 VAL cc_start: 0.9149 (t) cc_final: 0.8730 (p) REVERT: A 190 MET cc_start: 0.7489 (pmm) cc_final: 0.7125 (pmm) REVERT: A 194 MET cc_start: 0.7693 (pmm) cc_final: 0.7264 (pmm) REVERT: A 202 THR cc_start: 0.8771 (p) cc_final: 0.8321 (t) REVERT: A 321 MET cc_start: 0.8220 (ptp) cc_final: 0.7795 (mtm) REVERT: A 408 VAL cc_start: 0.9288 (t) cc_final: 0.8846 (p) REVERT: A 515 ILE cc_start: 0.9120 (mm) cc_final: 0.8843 (mm) REVERT: A 522 MET cc_start: 0.7147 (pmm) cc_final: 0.6937 (pmm) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.1076 time to fit residues: 14.1245 Evaluate side-chains 76 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.355 Evaluate side-chains 84 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.340 Fit side-chains REVERT: J 22 PHE cc_start: 0.8479 (m-80) cc_final: 0.8279 (m-10) REVERT: J 90 SER cc_start: 0.9251 (m) cc_final: 0.8869 (p) REVERT: J 385 MET cc_start: 0.8989 (mmt) cc_final: 0.8314 (mmp) REVERT: J 519 LEU cc_start: 0.9492 (pp) cc_final: 0.9246 (tt) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.0946 time to fit residues: 10.6483 Evaluate side-chains 66 residues out of total 433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.339 Evaluate side-chains 127 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 16 SER cc_start: 0.7349 (t) cc_final: 0.7075 (p) REVERT: K 119 GLN cc_start: 0.8467 (pm20) cc_final: 0.8256 (mt0) REVERT: K 364 CYS cc_start: 0.9044 (t) cc_final: 0.8771 (t) REVERT: K 423 TYR cc_start: 0.7937 (t80) cc_final: 0.7650 (t80) REVERT: K 501 ASN cc_start: 0.8705 (m110) cc_final: 0.8383 (m-40) REVERT: K 511 CYS cc_start: 0.8270 (m) cc_final: 0.7889 (m) REVERT: K 521 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7994 (mmtp) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1217 time to fit residues: 19.4268 Evaluate side-chains 96 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.343 Evaluate side-chains 131 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 23 ASP cc_start: 0.8533 (p0) cc_final: 0.8294 (p0) REVERT: D 31 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8985 (mt) REVERT: D 91 MET cc_start: 0.8719 (mmp) cc_final: 0.8492 (mmp) REVERT: D 198 ASP cc_start: 0.7517 (t0) cc_final: 0.7222 (t0) REVERT: D 204 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8893 (p) REVERT: D 267 ASP cc_start: 0.5150 (p0) cc_final: 0.4739 (p0) REVERT: D 333 ILE cc_start: 0.9217 (mm) cc_final: 0.8900 (mm) REVERT: D 364 PHE cc_start: 0.7661 (p90) cc_final: 0.7435 (p90) REVERT: D 395 ILE cc_start: 0.9215 (mm) cc_final: 0.8842 (pt) REVERT: D 396 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8520 (mm-30) REVERT: D 429 CYS cc_start: 0.8934 (m) cc_final: 0.8591 (t) REVERT: D 433 VAL cc_start: 0.9356 (t) cc_final: 0.9129 (p) REVERT: D 439 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8520 (mtmm) REVERT: D 483 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8614 (ttmm) REVERT: D 501 MET cc_start: 0.8142 (mmt) cc_final: 0.7696 (mmt) REVERT: D 508 GLU cc_start: 0.4781 (mt-10) cc_final: 0.4519 (pt0) REVERT: D 527 ILE cc_start: 0.9359 (mm) cc_final: 0.9152 (tp) outliers start: 19 outliers final: 3 residues processed: 126 average time/residue: 0.1223 time to fit residues: 19.4194 Evaluate side-chains 88 residues out of total 445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.356 Evaluate side-chains 99 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: M 37 ASP cc_start: 0.7926 (m-30) cc_final: 0.7680 (m-30) REVERT: M 130 TRP cc_start: 0.8052 (m-10) cc_final: 0.7781 (m-10) REVERT: M 134 THR cc_start: 0.9000 (m) cc_final: 0.8682 (p) REVERT: M 222 LYS cc_start: 0.8715 (mptt) cc_final: 0.8356 (mtmt) REVERT: M 358 LYS cc_start: 0.8873 (mttt) cc_final: 0.8585 (mtmt) REVERT: M 381 GLN cc_start: 0.9157 (mp10) cc_final: 0.8925 (mp10) REVERT: M 415 MET cc_start: 0.7965 (ttm) cc_final: 0.7575 (ttm) REVERT: M 417 MET cc_start: 0.8130 (mmp) cc_final: 0.7613 (tpp) REVERT: M 436 MET cc_start: 0.8691 (mmm) cc_final: 0.8212 (mmm) REVERT: M 445 MET cc_start: 0.8574 (tpp) cc_final: 0.8128 (tpp) REVERT: M 449 ILE cc_start: 0.9532 (mm) cc_final: 0.9220 (tt) REVERT: M 465 LEU cc_start: 0.8837 (tp) cc_final: 0.7784 (tp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1023 time to fit residues: 13.2597 Evaluate side-chains 78 residues out of total 412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.326 Evaluate side-chains 103 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 186 MET cc_start: 0.8795 (mmt) cc_final: 0.8111 (mmm) REVERT: N 271 GLN cc_start: 0.8086 (mt0) cc_final: 0.7465 (mp10) REVERT: N 355 MET cc_start: 0.8184 (tpt) cc_final: 0.7974 (tpp) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1102 time to fit residues: 14.5706 Evaluate side-chains 71 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.336 Evaluate side-chains 101 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 147 CYS cc_start: 0.9261 (m) cc_final: 0.8985 (p) REVERT: G 225 MET cc_start: 0.7515 (ttp) cc_final: 0.6914 (tmm) REVERT: G 281 THR cc_start: 0.7323 (m) cc_final: 0.6455 (m) REVERT: G 297 LEU cc_start: 0.9085 (mt) cc_final: 0.8797 (mt) REVERT: G 306 MET cc_start: 0.7994 (mmt) cc_final: 0.5874 (mmt) REVERT: G 377 LEU cc_start: 0.9121 (mm) cc_final: 0.8760 (mm) REVERT: G 387 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8478 (tm-30) REVERT: G 388 MET cc_start: 0.9045 (ptp) cc_final: 0.8405 (ptm) REVERT: G 389 GLU cc_start: 0.8171 (pp20) cc_final: 0.7744 (pp20) REVERT: G 430 MET cc_start: 0.7632 (tpt) cc_final: 0.7220 (tpp) REVERT: G 460 SER cc_start: 0.8716 (p) cc_final: 0.8279 (m) outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.0812 time to fit residues: 11.4825 Evaluate side-chains 75 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.345 Evaluate side-chains 125 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.349 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: P 51 LEU cc_start: 0.8224 (mt) cc_final: 0.7883 (pt) REVERT: P 59 MET cc_start: 0.8576 (tmm) cc_final: 0.8269 (tmm) REVERT: P 80 MET cc_start: 0.9353 (mmm) cc_final: 0.8692 (tpp) REVERT: P 132 ASP cc_start: 0.8772 (m-30) cc_final: 0.8363 (m-30) REVERT: P 133 MET cc_start: 0.8945 (mtm) cc_final: 0.8615 (tpp) REVERT: P 173 CYS cc_start: 0.8819 (p) cc_final: 0.8217 (m) REVERT: P 263 ASP cc_start: 0.8296 (m-30) cc_final: 0.7690 (m-30) REVERT: P 289 VAL cc_start: 0.8604 (t) cc_final: 0.8194 (t) REVERT: P 415 GLU cc_start: 0.8411 (mp0) cc_final: 0.7962 (mt-10) REVERT: P 416 MET cc_start: 0.7413 (mmp) cc_final: 0.7021 (mmp) REVERT: P 498 PRO cc_start: 0.8632 (Cg_exo) cc_final: 0.7896 (Cg_endo) REVERT: P 506 TYR cc_start: 0.8453 (m-80) cc_final: 0.7593 (m-80) REVERT: P 511 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8321 (tt0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1145 time to fit residues: 18.2682 Evaluate side-chains 94 residues out of total 452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.7753 > 50: distance: 0 - 1: 4.735 distance: 1 - 2: 5.722 distance: 1 - 4: 17.892 distance: 2 - 3: 18.083 distance: 2 - 9: 26.263 distance: 3 - 31: 30.156 distance: 4 - 5: 10.547 distance: 5 - 6: 6.142 distance: 6 - 7: 12.229 distance: 6 - 8: 6.561 distance: 9 - 10: 25.966 distance: 10 - 11: 23.937 distance: 10 - 13: 17.969 distance: 11 - 12: 43.332 distance: 11 - 17: 52.217 distance: 12 - 36: 37.964 distance: 13 - 14: 24.139 distance: 13 - 15: 8.294 distance: 14 - 16: 18.064 distance: 17 - 18: 25.059 distance: 18 - 19: 43.803 distance: 18 - 21: 40.084 distance: 19 - 20: 43.823 distance: 19 - 23: 11.255 distance: 20 - 43: 63.775 distance: 21 - 22: 25.546 distance: 23 - 24: 5.216 distance: 24 - 25: 14.106 distance: 24 - 27: 34.551 distance: 25 - 26: 18.935 distance: 25 - 31: 15.638 distance: 26 - 52: 25.336 distance: 27 - 28: 41.941 distance: 28 - 29: 37.774 distance: 28 - 30: 31.513 distance: 31 - 32: 16.220 distance: 32 - 33: 10.995 distance: 32 - 35: 24.656 distance: 33 - 34: 8.922 distance: 33 - 36: 27.249 distance: 34 - 60: 17.811 distance: 36 - 37: 9.975 distance: 37 - 38: 26.081 distance: 37 - 40: 29.614 distance: 38 - 39: 33.705 distance: 38 - 43: 24.794 distance: 39 - 67: 39.645 distance: 40 - 41: 48.845 distance: 40 - 42: 26.589 distance: 43 - 44: 24.621 distance: 44 - 45: 22.798 distance: 44 - 47: 44.064 distance: 45 - 46: 51.022 distance: 45 - 52: 31.698 distance: 47 - 48: 18.161 distance: 48 - 49: 10.524 distance: 49 - 50: 4.253 distance: 49 - 51: 20.772 distance: 52 - 53: 13.442 distance: 53 - 54: 18.074 distance: 53 - 56: 21.793 distance: 54 - 55: 12.837 distance: 54 - 60: 6.126 distance: 56 - 57: 7.314 distance: 57 - 58: 4.306 distance: 58 - 59: 21.546 distance: 60 - 61: 37.607 distance: 61 - 62: 33.702 distance: 61 - 64: 34.819 distance: 62 - 63: 8.189 distance: 62 - 67: 36.361 distance: 64 - 65: 12.748 distance: 64 - 66: 27.039 distance: 67 - 68: 32.398 distance: 68 - 69: 10.672 distance: 68 - 71: 13.503 distance: 69 - 70: 8.185 distance: 71 - 72: 9.320 distance: 72 - 73: 3.970 distance: 73 - 74: 3.130 distance: 74 - 75: 4.839 distance: 75 - 76: 12.292