Starting phenix.real_space_refine on Sun May 25 15:50:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iol_35621/05_2025/8iol_35621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iol_35621/05_2025/8iol_35621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iol_35621/05_2025/8iol_35621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iol_35621/05_2025/8iol_35621.map" model { file = "/net/cci-nas-00/data/ceres_data/8iol_35621/05_2025/8iol_35621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iol_35621/05_2025/8iol_35621.cif" } resolution = 2.9 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= 0.009 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 136 5.16 5 C 17504 2.51 5 N 4856 2.21 5 O 5060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 228 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27556 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3464 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 2 Chain: "C" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3464 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 419} Chain breaks: 2 Chain: "D" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 2 Chain: "G" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3464 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 419} Chain breaks: 2 Chain: "H" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 2 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3464 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 419} Chain breaks: 2 Chain: "F" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3425 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 2 Time building chain proxies: 15.20, per 1000 atoms: 0.55 Number of scatterers: 27556 At special positions: 0 Unit cell: (130, 130, 113.36, 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 136 16.00 O 5060 8.00 N 4856 7.00 C 17504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 189 " distance=2.04 Simple disulfide: pdb=" SG CYS D 169 " - pdb=" SG CYS D 189 " distance=2.04 Simple disulfide: pdb=" SG CYS H 169 " - pdb=" SG CYS H 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 189 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 4.4 seconds 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6368 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 24 sheets defined 48.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.830A pdb=" N ARG A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 150 through 160 removed outlier: 4.266A pdb=" N VAL A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.657A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 346 removed outlier: 3.921A pdb=" N THR A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 392 Processing helix chain 'A' and resid 410 through 431 Processing helix chain 'A' and resid 433 through 446 removed outlier: 6.358A pdb=" N GLY A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASP A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.781A pdb=" N TRP A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.582A pdb=" N TYR B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.625A pdb=" N THR B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 210 through 230 Processing helix chain 'B' and resid 243 through 257 Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.569A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 346 removed outlier: 3.928A pdb=" N ALA B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 383 through 392 Processing helix chain 'B' and resid 411 through 430 Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 46 through 59 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.830A pdb=" N ARG C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 150 through 160 removed outlier: 4.267A pdb=" N VAL C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 192 Processing helix chain 'C' and resid 210 through 230 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.657A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 346 removed outlier: 3.921A pdb=" N THR C 339 " --> pdb=" O ASP C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 392 Processing helix chain 'C' and resid 410 through 431 Processing helix chain 'C' and resid 433 through 446 removed outlier: 6.357A pdb=" N GLY C 439 " --> pdb=" O TYR C 435 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASP C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 459 removed outlier: 3.781A pdb=" N TRP C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 22 removed outlier: 3.582A pdb=" N TYR D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.569A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 346 removed outlier: 3.927A pdb=" N ALA D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 383 through 392 Processing helix chain 'D' and resid 411 through 430 Processing helix chain 'D' and resid 437 through 446 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 46 through 59 Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.829A pdb=" N ARG G 76 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'G' and resid 150 through 160 removed outlier: 4.266A pdb=" N VAL G 154 " --> pdb=" O HIS G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 192 Processing helix chain 'G' and resid 210 through 230 Processing helix chain 'G' and resid 243 through 257 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 270 through 285 Processing helix chain 'G' and resid 294 through 298 Processing helix chain 'G' and resid 307 through 319 removed outlier: 3.657A pdb=" N LEU G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 346 removed outlier: 3.921A pdb=" N THR G 339 " --> pdb=" O ASP G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 358 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 392 Processing helix chain 'G' and resid 410 through 431 Processing helix chain 'G' and resid 433 through 446 removed outlier: 6.358A pdb=" N GLY G 439 " --> pdb=" O TYR G 435 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP G 440 " --> pdb=" O ARG G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 459 removed outlier: 3.781A pdb=" N TRP G 459 " --> pdb=" O ALA G 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 22 removed outlier: 3.582A pdb=" N TYR H 22 " --> pdb=" O LYS H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 Processing helix chain 'H' and resid 103 through 105 No H-bonds generated for 'chain 'H' and resid 103 through 105' Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'H' and resid 152 through 160 Processing helix chain 'H' and resid 178 through 192 Processing helix chain 'H' and resid 210 through 230 Processing helix chain 'H' and resid 243 through 257 Processing helix chain 'H' and resid 266 through 270 Processing helix chain 'H' and resid 270 through 285 Processing helix chain 'H' and resid 294 through 298 Processing helix chain 'H' and resid 307 through 319 removed outlier: 3.569A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 346 removed outlier: 3.928A pdb=" N ALA H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 358 Processing helix chain 'H' and resid 383 through 392 Processing helix chain 'H' and resid 411 through 430 Processing helix chain 'H' and resid 437 through 446 Processing helix chain 'H' and resid 449 through 454 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 46 through 59 Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.830A pdb=" N ARG E 76 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.265A pdb=" N VAL E 154 " --> pdb=" O HIS E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 192 Processing helix chain 'E' and resid 210 through 230 Processing helix chain 'E' and resid 243 through 257 Processing helix chain 'E' and resid 266 through 270 Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 294 through 298 Processing helix chain 'E' and resid 307 through 319 removed outlier: 3.656A pdb=" N LEU E 311 " --> pdb=" O HIS E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 346 removed outlier: 3.921A pdb=" N THR E 339 " --> pdb=" O ASP E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 392 Processing helix chain 'E' and resid 410 through 431 Processing helix chain 'E' and resid 433 through 446 removed outlier: 6.357A pdb=" N GLY E 439 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASP E 440 " --> pdb=" O ARG E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 459 removed outlier: 3.781A pdb=" N TRP E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 22 removed outlier: 3.583A pdb=" N TYR F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 103 through 105 No H-bonds generated for 'chain 'F' and resid 103 through 105' Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.703A pdb=" N THR F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 160 Processing helix chain 'F' and resid 178 through 192 Processing helix chain 'F' and resid 210 through 230 Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 266 through 270 Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 294 through 298 Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.569A pdb=" N LEU F 311 " --> pdb=" O HIS F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 346 removed outlier: 3.928A pdb=" N ALA F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 383 through 392 Processing helix chain 'F' and resid 411 through 430 Processing helix chain 'F' and resid 437 through 446 Processing helix chain 'F' and resid 449 through 454 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 removed outlier: 5.689A pdb=" N CYS A 81 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA A 99 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A 38 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU A 132 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER A 40 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU A 130 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 6.590A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR A 197 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN A 238 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS A 235 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N MET A 263 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASP A 265 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS A 291 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS A 264 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 322 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS A 324 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 323 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER A 376 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 86 removed outlier: 5.690A pdb=" N CYS B 81 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA B 99 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG B 38 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU B 132 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER B 40 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU B 130 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 170 removed outlier: 7.438A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASP B 265 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS B 291 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS B 264 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 322 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N MET B 166 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE B 399 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY B 168 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 86 removed outlier: 5.689A pdb=" N CYS C 81 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA C 99 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG C 38 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU C 132 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER C 40 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU C 130 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 166 through 170 removed outlier: 6.590A pdb=" N LEU C 167 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS C 198 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS C 169 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR C 197 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN C 238 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS C 235 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N MET C 263 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU C 237 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASP C 265 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE C 262 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N HIS C 291 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS C 264 " --> pdb=" O HIS C 291 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS C 322 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS C 324 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 323 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER C 376 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET C 166 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 86 removed outlier: 5.690A pdb=" N CYS D 81 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA D 99 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG D 38 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU D 132 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER D 40 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU D 130 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 166 through 170 removed outlier: 7.439A pdb=" N THR D 197 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ASN D 238 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N HIS D 235 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET D 263 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 237 " --> pdb=" O MET D 263 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ASP D 265 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE D 262 " --> pdb=" O HIS D 289 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS D 291 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS D 264 " --> pdb=" O HIS D 291 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS D 322 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET D 166 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE D 399 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY D 168 " --> pdb=" O PHE D 399 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB4, first strand: chain 'G' and resid 80 through 86 removed outlier: 5.689A pdb=" N CYS G 81 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA G 99 " --> pdb=" O CYS G 81 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG G 38 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU G 132 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER G 40 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU G 130 " --> pdb=" O SER G 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 166 through 170 removed outlier: 6.590A pdb=" N LEU G 167 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS G 198 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N CYS G 169 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR G 197 " --> pdb=" O TYR G 236 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN G 238 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS G 235 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N MET G 263 " --> pdb=" O HIS G 235 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU G 237 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASP G 265 " --> pdb=" O LEU G 237 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE G 262 " --> pdb=" O HIS G 289 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS G 291 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS G 264 " --> pdb=" O HIS G 291 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS G 322 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS G 324 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU G 323 " --> pdb=" O VAL G 374 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER G 376 " --> pdb=" O LEU G 323 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET G 166 " --> pdb=" O LEU G 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 350 through 351 Processing sheet with id=AB7, first strand: chain 'H' and resid 80 through 86 removed outlier: 5.690A pdb=" N CYS H 81 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA H 99 " --> pdb=" O CYS H 81 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG H 38 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU H 132 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER H 40 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU H 130 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 166 through 170 removed outlier: 7.439A pdb=" N THR H 197 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN H 238 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N HIS H 235 " --> pdb=" O ILE H 261 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET H 263 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU H 237 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ASP H 265 " --> pdb=" O LEU H 237 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE H 262 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS H 291 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS H 264 " --> pdb=" O HIS H 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS H 322 " --> pdb=" O LEU H 288 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE H 399 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY H 168 " --> pdb=" O PHE H 399 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 350 through 351 Processing sheet with id=AC1, first strand: chain 'E' and resid 80 through 86 removed outlier: 5.689A pdb=" N CYS E 81 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA E 99 " --> pdb=" O CYS E 81 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG E 38 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU E 132 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER E 40 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU E 130 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 166 through 170 removed outlier: 6.590A pdb=" N LEU E 167 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LYS E 198 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS E 169 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR E 197 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN E 238 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS E 235 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N MET E 263 " --> pdb=" O HIS E 235 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU E 237 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ASP E 265 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE E 262 " --> pdb=" O HIS E 289 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS E 291 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N HIS E 264 " --> pdb=" O HIS E 291 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS E 322 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS E 324 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU E 323 " --> pdb=" O VAL E 374 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER E 376 " --> pdb=" O LEU E 323 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET E 166 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AC4, first strand: chain 'F' and resid 80 through 86 removed outlier: 5.690A pdb=" N CYS F 81 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA F 99 " --> pdb=" O CYS F 81 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG F 38 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU F 132 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER F 40 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU F 130 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 166 through 170 removed outlier: 7.438A pdb=" N THR F 197 " --> pdb=" O TYR F 236 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN F 238 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N HIS F 235 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET F 263 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU F 237 " --> pdb=" O MET F 263 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASP F 265 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE F 262 " --> pdb=" O HIS F 289 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS F 291 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS F 264 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS F 322 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N MET F 166 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE F 399 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY F 168 " --> pdb=" O PHE F 399 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 350 through 351 1272 hydrogen bonds defined for protein. 3576 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: 9.63 Time building geometry restraints manager: 7.46 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: 9185 1.34 - 1.46: 6628 1.46 - 1.58: 12203 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 28232 Sorted by residual: bond pdb=" C PHE B 137 " pdb=" N PRO B 138 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" C PHE F 137 " pdb=" N PRO F 138 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.25e-02 6.40e+03 1.12e+01 bond pdb=" C TYR H 26 " pdb=" N THR H 27 " ideal model delta sigma weight residual 1.333 1.300 0.032 1.59e-02 3.96e+03 4.06e+00 bond pdb=" C TYR F 26 " pdb=" N THR F 27 " ideal model delta sigma weight residual 1.333 1.300 0.032 1.59e-02 3.96e+03 4.06e+00 bond pdb=" C TYR D 26 " pdb=" N THR D 27 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.59e-02 3.96e+03 4.00e+00 ... (remaining 28227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 37445 2.31 - 4.62: 689 4.62 - 6.93: 62 6.93 - 9.24: 14 9.24 - 11.55: 10 Bond angle restraints: 38220 Sorted by residual: angle pdb=" C PHE B 137 " pdb=" N PRO B 138 " pdb=" CA PRO B 138 " ideal model delta sigma weight residual 120.21 113.15 7.06 9.60e-01 1.09e+00 5.40e+01 angle pdb=" C PHE F 137 " pdb=" N PRO F 138 " pdb=" CA PRO F 138 " ideal model delta sigma weight residual 120.21 113.20 7.01 9.60e-01 1.09e+00 5.32e+01 angle pdb=" C GLY C 341 " pdb=" N PHE C 342 " pdb=" CA PHE C 342 " ideal model delta sigma weight residual 121.58 114.55 7.03 1.95e+00 2.63e-01 1.30e+01 angle pdb=" C GLY E 341 " pdb=" N PHE E 342 " pdb=" CA PHE E 342 " ideal model delta sigma weight residual 121.58 114.56 7.02 1.95e+00 2.63e-01 1.30e+01 angle pdb=" C GLY A 341 " pdb=" N PHE A 342 " pdb=" CA PHE A 342 " ideal model delta sigma weight residual 121.58 114.56 7.02 1.95e+00 2.63e-01 1.30e+01 ... (remaining 38215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 14808 16.21 - 32.42: 1511 32.42 - 48.62: 234 48.62 - 64.83: 58 64.83 - 81.04: 13 Dihedral angle restraints: 16624 sinusoidal: 6660 harmonic: 9964 Sorted by residual: dihedral pdb=" CA PRO D 173 " pdb=" C PRO D 173 " pdb=" N LYS D 174 " pdb=" CA LYS D 174 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PRO B 173 " pdb=" C PRO B 173 " pdb=" N LYS B 174 " pdb=" CA LYS B 174 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA PRO H 173 " pdb=" C PRO H 173 " pdb=" N LYS H 174 " pdb=" CA LYS H 174 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 16621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2327 0.039 - 0.078: 1229 0.078 - 0.117: 405 0.117 - 0.156: 119 0.156 - 0.195: 8 Chirality restraints: 4088 Sorted by residual: chirality pdb=" CA LYS D 172 " pdb=" N LYS D 172 " pdb=" C LYS D 172 " pdb=" CB LYS D 172 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CA LYS B 172 " pdb=" N LYS B 172 " pdb=" C LYS B 172 " pdb=" CB LYS B 172 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA LYS H 172 " pdb=" N LYS H 172 " pdb=" C LYS H 172 " pdb=" CB LYS H 172 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 4085 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 155 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C GLU C 155 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU C 155 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG C 156 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 142 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C VAL H 142 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL H 142 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS H 143 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 411 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO B 412 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " -0.021 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 945 2.69 - 3.24: 28764 3.24 - 3.80: 45983 3.80 - 4.35: 62079 4.35 - 4.90: 104946 Nonbonded interactions: 242717 Sorted by model distance: nonbonded pdb=" OD1 ASP G 199 " pdb=" NE2 HIS G 235 " model vdw 2.138 3.120 nonbonded pdb=" OD1 ASP A 199 " pdb=" NE2 HIS A 235 " model vdw 2.139 3.120 nonbonded pdb=" OD1 ASP C 199 " pdb=" NE2 HIS C 235 " model vdw 2.139 3.120 nonbonded pdb=" OD1 ASP E 199 " pdb=" NE2 HIS E 235 " model vdw 2.139 3.120 nonbonded pdb=" O ASP B 335 " pdb=" OG SER B 338 " model vdw 2.166 3.040 ... (remaining 242712 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.040 Extract box with map and model: 1.030 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 57.630 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 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 : 0.010 0.050 28236 Z= 0.436 Angle : 0.800 11.548 38228 Z= 0.441 Chirality : 0.051 0.195 4088 Planarity : 0.004 0.037 4992 Dihedral : 13.147 81.041 10244 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.39 % Allowed : 5.08 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.12), residues: 3468 helix: -1.67 (0.11), residues: 1412 sheet: -1.46 (0.20), residues: 476 loop : -2.58 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 211 HIS 0.005 0.001 HIS D 383 PHE 0.023 0.002 PHE D 342 TYR 0.009 0.001 TYR D 182 ARG 0.005 0.000 ARG F 212 Details of bonding type rmsd hydrogen bonds : bond 0.17518 ( 1272) hydrogen bonds : angle 7.64363 ( 3576) SS BOND : bond 0.00427 ( 4) SS BOND : angle 3.48515 ( 8) covalent geometry : bond 0.00992 (28232) covalent geometry : angle 0.79822 (38220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 548 time to evaluate : 3.170 Fit side-chains REVERT: A 25 ASP cc_start: 0.6248 (p0) cc_final: 0.5905 (t70) REVERT: A 40 SER cc_start: 0.8540 (t) cc_final: 0.8281 (t) REVERT: A 78 LYS cc_start: 0.6588 (mttp) cc_final: 0.6272 (ptpp) REVERT: A 80 LYS cc_start: 0.7039 (mttp) cc_final: 0.6362 (mttp) REVERT: A 85 GLU cc_start: 0.7827 (pt0) cc_final: 0.7591 (pt0) REVERT: A 128 ARG cc_start: 0.7889 (ptt180) cc_final: 0.7427 (ptt90) REVERT: A 184 ARG cc_start: 0.7499 (mtt90) cc_final: 0.7087 (tpm170) REVERT: A 191 ARG cc_start: 0.6812 (tpt90) cc_final: 0.6404 (tpm170) REVERT: A 206 GLN cc_start: 0.8487 (mp10) cc_final: 0.8279 (mp10) REVERT: A 256 GLU cc_start: 0.7109 (tt0) cc_final: 0.6823 (tt0) REVERT: A 301 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7626 (mm110) REVERT: A 336 LYS cc_start: 0.6736 (pttt) cc_final: 0.6488 (pttp) REVERT: A 340 LEU cc_start: 0.7155 (mt) cc_final: 0.6492 (mt) REVERT: A 348 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 352 GLU cc_start: 0.7222 (mp0) cc_final: 0.6921 (mp0) REVERT: A 354 ASP cc_start: 0.6015 (t0) cc_final: 0.5673 (p0) REVERT: B 127 ILE cc_start: 0.8078 (mt) cc_final: 0.7422 (tt) REVERT: B 166 MET cc_start: 0.7304 (mtt) cc_final: 0.6914 (mtm) REVERT: B 206 GLN cc_start: 0.8546 (mt0) cc_final: 0.8334 (mp10) REVERT: B 226 GLN cc_start: 0.7376 (mt0) cc_final: 0.7111 (mt0) REVERT: B 252 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 256 GLU cc_start: 0.7178 (tt0) cc_final: 0.6889 (tt0) REVERT: B 279 LYS cc_start: 0.8172 (mttm) cc_final: 0.7840 (mttm) REVERT: B 301 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7682 (mm110) REVERT: B 355 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7481 (mmm-85) REVERT: B 391 PHE cc_start: 0.6908 (m-80) cc_final: 0.6569 (m-10) REVERT: C 25 ASP cc_start: 0.6328 (p0) cc_final: 0.5843 (t70) REVERT: C 30 ASP cc_start: 0.7456 (m-30) cc_final: 0.7082 (m-30) REVERT: C 40 SER cc_start: 0.8557 (t) cc_final: 0.8310 (t) REVERT: C 78 LYS cc_start: 0.6576 (mttp) cc_final: 0.6249 (ptpp) REVERT: C 80 LYS cc_start: 0.7039 (mttp) cc_final: 0.6376 (mttp) REVERT: C 85 GLU cc_start: 0.7842 (pt0) cc_final: 0.7617 (pt0) REVERT: C 128 ARG cc_start: 0.7803 (ptt180) cc_final: 0.7365 (ptt90) REVERT: C 166 MET cc_start: 0.8487 (mtt) cc_final: 0.8263 (mtm) REVERT: C 184 ARG cc_start: 0.7566 (mtt90) cc_final: 0.7164 (tpm170) REVERT: C 191 ARG cc_start: 0.6807 (tpt90) cc_final: 0.6366 (tpm170) REVERT: C 206 GLN cc_start: 0.8555 (mp10) cc_final: 0.8311 (mp10) REVERT: C 256 GLU cc_start: 0.7075 (tt0) cc_final: 0.6803 (tt0) REVERT: C 301 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7531 (mm110) REVERT: C 336 LYS cc_start: 0.6718 (pttt) cc_final: 0.6471 (pttp) REVERT: C 340 LEU cc_start: 0.7200 (mt) cc_final: 0.6547 (mt) REVERT: C 348 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7294 (mm-30) REVERT: C 352 GLU cc_start: 0.7213 (mp0) cc_final: 0.6919 (mp0) REVERT: C 354 ASP cc_start: 0.6022 (t0) cc_final: 0.5660 (p0) REVERT: C 383 HIS cc_start: 0.7518 (m170) cc_final: 0.7203 (m170) REVERT: D 206 GLN cc_start: 0.8503 (mt0) cc_final: 0.8291 (mp10) REVERT: D 226 GLN cc_start: 0.7367 (mt0) cc_final: 0.7058 (mt0) REVERT: D 252 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 256 GLU cc_start: 0.7183 (tt0) cc_final: 0.6876 (tt0) REVERT: D 279 LYS cc_start: 0.8234 (mttm) cc_final: 0.7875 (mttm) REVERT: D 301 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7594 (mm110) REVERT: D 355 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7469 (mmm-85) REVERT: D 391 PHE cc_start: 0.6882 (m-80) cc_final: 0.6562 (m-10) REVERT: G 25 ASP cc_start: 0.6287 (p0) cc_final: 0.5867 (t70) REVERT: G 40 SER cc_start: 0.8571 (t) cc_final: 0.8326 (t) REVERT: G 78 LYS cc_start: 0.6573 (mttp) cc_final: 0.6203 (ptpp) REVERT: G 80 LYS cc_start: 0.7034 (mttp) cc_final: 0.6356 (mttp) REVERT: G 85 GLU cc_start: 0.7883 (pt0) cc_final: 0.7672 (pt0) REVERT: G 128 ARG cc_start: 0.7817 (ptt180) cc_final: 0.7409 (ptt90) REVERT: G 191 ARG cc_start: 0.6887 (tpt90) cc_final: 0.6454 (tpm170) REVERT: G 206 GLN cc_start: 0.8582 (mp10) cc_final: 0.8367 (mp10) REVERT: G 256 GLU cc_start: 0.7101 (tt0) cc_final: 0.6839 (tt0) REVERT: G 301 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7623 (mm110) REVERT: G 336 LYS cc_start: 0.6694 (pttt) cc_final: 0.6458 (pttp) REVERT: G 340 LEU cc_start: 0.7191 (mt) cc_final: 0.6526 (mt) REVERT: G 348 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7280 (mm-30) REVERT: G 352 GLU cc_start: 0.7274 (mp0) cc_final: 0.6985 (mp0) REVERT: G 354 ASP cc_start: 0.5934 (t0) cc_final: 0.5616 (p0) REVERT: H 188 GLU cc_start: 0.6994 (tp30) cc_final: 0.6669 (pt0) REVERT: H 206 GLN cc_start: 0.8499 (mt0) cc_final: 0.8287 (mp10) REVERT: H 226 GLN cc_start: 0.7367 (mt0) cc_final: 0.7059 (mt0) REVERT: H 252 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7562 (mm-30) REVERT: H 256 GLU cc_start: 0.7182 (tt0) cc_final: 0.6876 (tt0) REVERT: H 301 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7602 (mm110) REVERT: H 355 ARG cc_start: 0.7770 (mmm-85) cc_final: 0.7487 (mmm-85) REVERT: H 391 PHE cc_start: 0.6884 (m-80) cc_final: 0.6570 (m-10) REVERT: E 25 ASP cc_start: 0.6248 (p0) cc_final: 0.5904 (t70) REVERT: E 40 SER cc_start: 0.8541 (t) cc_final: 0.8284 (t) REVERT: E 78 LYS cc_start: 0.6590 (mttp) cc_final: 0.6276 (ptpp) REVERT: E 80 LYS cc_start: 0.7042 (mttp) cc_final: 0.6364 (mttp) REVERT: E 85 GLU cc_start: 0.7822 (pt0) cc_final: 0.7586 (pt0) REVERT: E 128 ARG cc_start: 0.7886 (ptt180) cc_final: 0.7429 (ptt90) REVERT: E 184 ARG cc_start: 0.7582 (mtt90) cc_final: 0.7177 (tpm170) REVERT: E 191 ARG cc_start: 0.6810 (tpt90) cc_final: 0.6383 (tpm170) REVERT: E 206 GLN cc_start: 0.8459 (mp10) cc_final: 0.8235 (mp10) REVERT: E 256 GLU cc_start: 0.7104 (tt0) cc_final: 0.6821 (tt0) REVERT: E 301 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7635 (mm110) REVERT: E 336 LYS cc_start: 0.6723 (pttt) cc_final: 0.6485 (pttp) REVERT: E 340 LEU cc_start: 0.7155 (mt) cc_final: 0.6498 (mt) REVERT: E 348 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7270 (mm-30) REVERT: E 352 GLU cc_start: 0.7223 (mp0) cc_final: 0.6926 (mp0) REVERT: E 354 ASP cc_start: 0.6011 (t0) cc_final: 0.5673 (p0) REVERT: F 166 MET cc_start: 0.7231 (mtt) cc_final: 0.6862 (mtm) REVERT: F 206 GLN cc_start: 0.8544 (mt0) cc_final: 0.8337 (mp10) REVERT: F 226 GLN cc_start: 0.7389 (mt0) cc_final: 0.7118 (mt0) REVERT: F 252 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7561 (mm-30) REVERT: F 256 GLU cc_start: 0.7176 (tt0) cc_final: 0.6889 (tt0) REVERT: F 279 LYS cc_start: 0.8244 (mttm) cc_final: 0.7900 (mttm) REVERT: F 301 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7683 (mm110) REVERT: F 355 ARG cc_start: 0.7754 (mmm-85) cc_final: 0.7475 (mmm-85) REVERT: F 391 PHE cc_start: 0.6934 (m-80) cc_final: 0.6608 (m-10) outliers start: 11 outliers final: 0 residues processed: 556 average time/residue: 1.5790 time to fit residues: 1000.7857 Evaluate side-chains 416 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 chunk 105 optimal weight: 0.3980 chunk 165 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 316 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 209 GLN B 92 ASN B 226 GLN B 264 HIS B 350 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 209 GLN D 92 ASN D 226 GLN D 264 HIS D 350 HIS D 398 GLN G 204 ASN H 92 ASN H 226 GLN H 264 HIS H 350 HIS H 398 GLN E 209 GLN F 92 ASN F 226 GLN F 264 HIS F 350 HIS F 398 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.176556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.135343 restraints weight = 28319.731| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.02 r_work: 0.3120 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28236 Z= 0.126 Angle : 0.589 7.438 38228 Z= 0.304 Chirality : 0.043 0.149 4088 Planarity : 0.004 0.038 4992 Dihedral : 4.999 23.557 3812 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.54 % Allowed : 11.69 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3468 helix: 0.30 (0.13), residues: 1484 sheet: -1.02 (0.22), residues: 444 loop : -1.95 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 382 HIS 0.006 0.001 HIS E 289 PHE 0.033 0.002 PHE C 342 TYR 0.008 0.001 TYR B 162 ARG 0.005 0.001 ARG A 302 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 1272) hydrogen bonds : angle 5.41153 ( 3576) SS BOND : bond 0.00150 ( 4) SS BOND : angle 1.10494 ( 8) covalent geometry : bond 0.00285 (28232) covalent geometry : angle 0.58883 (38220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 480 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6507 (p0) cc_final: 0.6082 (t70) REVERT: A 74 MET cc_start: 0.5995 (ttm) cc_final: 0.5748 (mpt) REVERT: A 80 LYS cc_start: 0.7529 (mttp) cc_final: 0.7250 (mttp) REVERT: A 128 ARG cc_start: 0.8418 (ptt180) cc_final: 0.8098 (ptt90) REVERT: A 153 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8189 (mm110) REVERT: A 301 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8547 (mm110) REVERT: A 302 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8105 (mtp85) REVERT: A 340 LEU cc_start: 0.8166 (mt) cc_final: 0.7596 (mt) REVERT: B 21 TYR cc_start: 0.8527 (m-80) cc_final: 0.8294 (m-80) REVERT: B 57 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 127 ILE cc_start: 0.8669 (mt) cc_final: 0.8173 (tt) REVERT: B 162 TYR cc_start: 0.7841 (m-80) cc_final: 0.7318 (m-80) REVERT: B 166 MET cc_start: 0.7764 (mtt) cc_final: 0.7494 (mtm) REVERT: B 184 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7740 (tpm170) REVERT: B 201 GLU cc_start: 0.7252 (pm20) cc_final: 0.7022 (pm20) REVERT: B 226 GLN cc_start: 0.8091 (mt0) cc_final: 0.7813 (mt0) REVERT: B 256 GLU cc_start: 0.8079 (tt0) cc_final: 0.7877 (tt0) REVERT: B 364 ASP cc_start: 0.7903 (m-30) cc_final: 0.7676 (m-30) REVERT: B 384 MET cc_start: 0.6912 (tpp) cc_final: 0.6712 (tpp) REVERT: C 25 ASP cc_start: 0.6532 (p0) cc_final: 0.6090 (t70) REVERT: C 80 LYS cc_start: 0.7679 (mttp) cc_final: 0.7355 (mttp) REVERT: C 128 ARG cc_start: 0.8412 (ptt180) cc_final: 0.8082 (ptt90) REVERT: C 153 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8315 (mm110) REVERT: C 301 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8522 (mm110) REVERT: C 340 LEU cc_start: 0.8195 (mt) cc_final: 0.7797 (mt) REVERT: C 344 ASP cc_start: 0.7710 (m-30) cc_final: 0.7454 (t70) REVERT: D 57 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7548 (mm-30) REVERT: D 127 ILE cc_start: 0.8745 (mt) cc_final: 0.8276 (tt) REVERT: D 162 TYR cc_start: 0.7722 (m-80) cc_final: 0.7262 (m-80) REVERT: D 166 MET cc_start: 0.7734 (mtt) cc_final: 0.7508 (mtm) REVERT: D 184 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7782 (tpm170) REVERT: D 201 GLU cc_start: 0.7247 (pm20) cc_final: 0.7003 (pm20) REVERT: D 256 GLU cc_start: 0.8003 (tt0) cc_final: 0.7793 (tt0) REVERT: D 364 ASP cc_start: 0.7905 (m-30) cc_final: 0.7688 (m-30) REVERT: D 384 MET cc_start: 0.6910 (tpp) cc_final: 0.6708 (tpp) REVERT: G 25 ASP cc_start: 0.6509 (p0) cc_final: 0.6067 (t70) REVERT: G 74 MET cc_start: 0.5981 (ttm) cc_final: 0.5733 (mpt) REVERT: G 80 LYS cc_start: 0.7620 (mttp) cc_final: 0.7363 (mttp) REVERT: G 128 ARG cc_start: 0.8405 (ptt180) cc_final: 0.8089 (ptt90) REVERT: G 153 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8233 (mm110) REVERT: G 184 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8285 (tpm170) REVERT: G 301 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8506 (mm110) REVERT: G 302 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8105 (mtp85) REVERT: G 340 LEU cc_start: 0.8184 (mt) cc_final: 0.7607 (mt) REVERT: H 57 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7626 (mm-30) REVERT: H 127 ILE cc_start: 0.8722 (mt) cc_final: 0.8248 (tt) REVERT: H 166 MET cc_start: 0.7738 (mtt) cc_final: 0.7518 (mtm) REVERT: H 184 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7809 (tpm170) REVERT: H 201 GLU cc_start: 0.7251 (pm20) cc_final: 0.7008 (pm20) REVERT: H 231 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7205 (mm-30) REVERT: H 256 GLU cc_start: 0.8017 (tt0) cc_final: 0.7806 (tt0) REVERT: H 364 ASP cc_start: 0.7906 (m-30) cc_final: 0.7674 (m-30) REVERT: E 25 ASP cc_start: 0.6512 (p0) cc_final: 0.6088 (t70) REVERT: E 74 MET cc_start: 0.6028 (ttm) cc_final: 0.5763 (mpt) REVERT: E 80 LYS cc_start: 0.7538 (mttp) cc_final: 0.7269 (mttp) REVERT: E 128 ARG cc_start: 0.8449 (ptt180) cc_final: 0.8124 (ptt90) REVERT: E 153 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8207 (mm110) REVERT: E 301 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8524 (mm110) REVERT: E 302 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8160 (mtp85) REVERT: E 340 LEU cc_start: 0.8166 (mt) cc_final: 0.7600 (mt) REVERT: F 57 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7579 (mm-30) REVERT: F 127 ILE cc_start: 0.8749 (mt) cc_final: 0.8272 (tt) REVERT: F 166 MET cc_start: 0.7736 (mtt) cc_final: 0.7469 (mtm) REVERT: F 184 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7760 (tpm170) REVERT: F 201 GLU cc_start: 0.7276 (pm20) cc_final: 0.7040 (pm20) REVERT: F 226 GLN cc_start: 0.8086 (mt0) cc_final: 0.7804 (mt0) REVERT: F 256 GLU cc_start: 0.8057 (tt0) cc_final: 0.7855 (tt0) REVERT: F 364 ASP cc_start: 0.7917 (m-30) cc_final: 0.7688 (m-30) outliers start: 44 outliers final: 10 residues processed: 502 average time/residue: 1.5181 time to fit residues: 875.2763 Evaluate side-chains 393 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 383 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 191 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6069 > 50: distance: 25 - 165: 12.322 distance: 28 - 162: 13.025 distance: 38 - 149: 36.112 distance: 41 - 146: 15.424 distance: 106 - 110: 7.825 distance: 110 - 111: 9.066 distance: 111 - 114: 13.661 distance: 112 - 113: 20.275 distance: 112 - 118: 8.611 distance: 113 - 250: 19.754 distance: 114 - 115: 10.271 distance: 115 - 116: 11.225 distance: 115 - 117: 3.225 distance: 118 - 119: 5.861 distance: 119 - 120: 7.815 distance: 120 - 121: 5.239 distance: 120 - 129: 11.145 distance: 122 - 123: 14.384 distance: 123 - 124: 18.183 distance: 124 - 125: 5.174 distance: 125 - 126: 5.204 distance: 126 - 127: 3.939 distance: 126 - 128: 5.745 distance: 130 - 131: 4.911 distance: 130 - 133: 3.898 distance: 131 - 132: 3.112 distance: 131 - 137: 5.697 distance: 134 - 135: 7.666 distance: 134 - 136: 4.495 distance: 137 - 138: 7.389 distance: 138 - 139: 14.478 distance: 138 - 141: 5.910 distance: 139 - 140: 8.989 distance: 139 - 146: 6.570 distance: 142 - 143: 7.557 distance: 143 - 144: 5.967 distance: 143 - 145: 10.537 distance: 146 - 147: 16.413 distance: 147 - 148: 30.216 distance: 147 - 150: 29.947 distance: 148 - 149: 15.069 distance: 148 - 154: 13.125 distance: 150 - 151: 13.219 distance: 151 - 152: 24.992 distance: 151 - 153: 9.731 distance: 154 - 155: 16.775 distance: 155 - 156: 11.321 distance: 155 - 158: 10.428 distance: 156 - 157: 9.010 distance: 156 - 162: 15.792 distance: 158 - 159: 4.507 distance: 158 - 160: 15.136 distance: 162 - 163: 10.974 distance: 163 - 164: 14.344 distance: 163 - 166: 7.009 distance: 164 - 165: 5.737 distance: 164 - 173: 20.722 distance: 166 - 167: 11.528 distance: 167 - 168: 8.187 distance: 168 - 169: 10.593 distance: 169 - 170: 15.338 distance: 170 - 171: 10.825 distance: 170 - 172: 17.523 distance: 173 - 174: 5.552 distance: 174 - 175: 14.485 distance: 174 - 177: 6.204 distance: 175 - 176: 19.767 distance: 175 - 184: 15.010 distance: 177 - 178: 7.731 distance: 178 - 179: 12.437 distance: 178 - 180: 9.899 distance: 179 - 181: 12.383 distance: 180 - 182: 10.546 distance: 181 - 183: 5.723 distance: 182 - 183: 7.210 distance: 184 - 185: 8.631 distance: 184 - 190: 10.447 distance: 185 - 186: 9.143 distance: 185 - 188: 4.937 distance: 186 - 187: 4.599 distance: 186 - 191: 3.326 distance: 187 - 210: 5.145 distance: 189 - 190: 5.597 distance: 192 - 193: 3.322 distance: 193 - 194: 3.024 distance: 194 - 217: 5.630 distance: 195 - 196: 4.716 distance: 195 - 197: 8.415