Starting phenix.real_space_refine on Mon Aug 25 09:44:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iol_35621/08_2025/8iol_35621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iol_35621/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8iol_35621/08_2025/8iol_35621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iol_35621/08_2025/8iol_35621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iol_35621/08_2025/8iol_35621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iol_35621/08_2025/8iol_35621.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.24, per 1000 atoms: 0.19 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: 2.22 Conformation dependent library (CDL) restraints added in 951.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.17 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: 4.78 Time building geometry restraints manager: 2.88 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'F' } 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: 0.580 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.240 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG F 212 TYR 0.009 0.001 TYR D 182 PHE 0.023 0.002 PHE D 342 TRP 0.017 0.002 TRP F 211 HIS 0.005 0.001 HIS D 383 Details of bonding type rmsd covalent geometry : bond 0.00992 (28232) covalent geometry : angle 0.79822 (38220) SS BOND : bond 0.00427 ( 4) SS BOND : angle 3.48515 ( 8) hydrogen bonds : bond 0.17518 ( 1272) hydrogen bonds : angle 7.64363 ( 3576) *********************** 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 : 1.049 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: 0.8309 (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: 0.6497 (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: 0.6607 (m-10) outliers start: 11 outliers final: 0 residues processed: 556 average time/residue: 0.7697 time to fit residues: 485.9277 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 : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN B 92 ASN B 226 GLN B 264 HIS B 295 HIS B 350 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN D 92 ASN D 226 GLN D 264 HIS D 350 HIS D 398 GLN H 92 ASN H 226 GLN H 264 HIS H 350 HIS ** H 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 92 ASN F 226 GLN F 264 HIS F 350 HIS ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.173141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.131779 restraints weight = 28495.487| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.00 r_work: 0.3051 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28236 Z= 0.178 Angle : 0.635 8.137 38228 Z= 0.328 Chirality : 0.045 0.179 4088 Planarity : 0.005 0.041 4992 Dihedral : 5.194 25.367 3812 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.47 % Allowed : 12.25 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.13), residues: 3468 helix: 0.09 (0.13), residues: 1484 sheet: -0.89 (0.21), residues: 484 loop : -2.00 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 302 TYR 0.010 0.001 TYR G 26 PHE 0.033 0.002 PHE G 342 TRP 0.011 0.001 TRP F 382 HIS 0.007 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00419 (28232) covalent geometry : angle 0.63427 (38220) SS BOND : bond 0.00313 ( 4) SS BOND : angle 1.57298 ( 8) hydrogen bonds : bond 0.04412 ( 1272) hydrogen bonds : angle 5.55862 ( 3576) *********************** 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 493 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 451 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6476 (p0) cc_final: 0.6045 (t70) REVERT: A 74 MET cc_start: 0.6096 (ttm) cc_final: 0.5745 (mpt) REVERT: A 78 LYS cc_start: 0.7241 (mttp) cc_final: 0.7031 (ptpp) REVERT: A 80 LYS cc_start: 0.7599 (mttp) cc_final: 0.7179 (mttp) REVERT: A 128 ARG cc_start: 0.8433 (ptt180) cc_final: 0.8068 (ptt90) REVERT: A 153 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8187 (mm110) REVERT: A 191 ARG cc_start: 0.7432 (tpt90) cc_final: 0.7197 (tpm170) REVERT: A 301 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8547 (mm110) REVERT: A 302 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8055 (mtp85) REVERT: A 340 LEU cc_start: 0.8190 (mt) cc_final: 0.7689 (mt) REVERT: B 21 TYR cc_start: 0.8568 (m-80) cc_final: 0.8356 (m-80) REVERT: B 124 PHE cc_start: 0.8563 (t80) cc_final: 0.8346 (t80) REVERT: B 127 ILE cc_start: 0.8677 (mt) cc_final: 0.8154 (tt) REVERT: B 166 MET cc_start: 0.7988 (mtt) cc_final: 0.7722 (mtm) REVERT: B 184 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.7779 (tpm170) REVERT: B 201 GLU cc_start: 0.7304 (pm20) cc_final: 0.6986 (pm20) REVERT: B 226 GLN cc_start: 0.8121 (mt0) cc_final: 0.7729 (tt0) REVERT: B 231 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: B 256 GLU cc_start: 0.8107 (tt0) cc_final: 0.7884 (tt0) REVERT: B 364 ASP cc_start: 0.7933 (m-30) cc_final: 0.7683 (m-30) REVERT: C 25 ASP cc_start: 0.6512 (p0) cc_final: 0.6061 (t70) REVERT: C 74 MET cc_start: 0.6127 (ttm) cc_final: 0.5793 (mpt) REVERT: C 78 LYS cc_start: 0.7323 (mttp) cc_final: 0.7116 (ptpp) REVERT: C 80 LYS cc_start: 0.7593 (mttp) cc_final: 0.7182 (mttp) REVERT: C 128 ARG cc_start: 0.8450 (ptt180) cc_final: 0.8095 (ptt90) REVERT: C 153 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8213 (mm110) REVERT: C 191 ARG cc_start: 0.7364 (tpt90) cc_final: 0.7151 (tpm170) REVERT: C 301 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8532 (mm110) REVERT: C 302 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: C 340 LEU cc_start: 0.8211 (mt) cc_final: 0.7697 (mt) REVERT: D 21 TYR cc_start: 0.8555 (m-80) cc_final: 0.8351 (m-80) REVERT: D 57 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7544 (mm-30) REVERT: D 127 ILE cc_start: 0.8724 (mt) cc_final: 0.8283 (tt) REVERT: D 184 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7798 (tpm170) REVERT: D 201 GLU cc_start: 0.7302 (pm20) cc_final: 0.6988 (pm20) REVERT: D 226 GLN cc_start: 0.8122 (mt0) cc_final: 0.7732 (tt0) REVERT: D 231 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: D 256 GLU cc_start: 0.8006 (tt0) cc_final: 0.7786 (tt0) REVERT: D 364 ASP cc_start: 0.7909 (m-30) cc_final: 0.7660 (m-30) REVERT: G 25 ASP cc_start: 0.6472 (p0) cc_final: 0.6041 (t70) REVERT: G 74 MET cc_start: 0.6121 (ttm) cc_final: 0.5745 (mpt) REVERT: G 78 LYS cc_start: 0.7240 (mttp) cc_final: 0.7020 (ptpp) REVERT: G 80 LYS cc_start: 0.7589 (mttp) cc_final: 0.7164 (mttp) REVERT: G 128 ARG cc_start: 0.8403 (ptt180) cc_final: 0.8053 (ptt90) REVERT: G 153 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8206 (mm110) REVERT: G 191 ARG cc_start: 0.7425 (tpt90) cc_final: 0.7212 (tpm170) REVERT: G 301 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8531 (mm110) REVERT: G 302 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.8076 (mtp85) REVERT: G 340 LEU cc_start: 0.8195 (mt) cc_final: 0.7704 (mt) REVERT: H 21 TYR cc_start: 0.8572 (m-80) cc_final: 0.8361 (m-80) REVERT: H 127 ILE cc_start: 0.8722 (mt) cc_final: 0.8271 (tt) REVERT: H 184 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7843 (tpm170) REVERT: H 201 GLU cc_start: 0.7300 (pm20) cc_final: 0.7088 (pm20) REVERT: H 226 GLN cc_start: 0.8101 (mt0) cc_final: 0.7716 (tt0) REVERT: H 256 GLU cc_start: 0.8016 (tt0) cc_final: 0.7793 (tt0) REVERT: H 364 ASP cc_start: 0.7919 (m-30) cc_final: 0.7673 (m-30) REVERT: E 25 ASP cc_start: 0.6484 (p0) cc_final: 0.6057 (t70) REVERT: E 74 MET cc_start: 0.6146 (ttm) cc_final: 0.5789 (mpt) REVERT: E 78 LYS cc_start: 0.7245 (mttp) cc_final: 0.7040 (ptpp) REVERT: E 80 LYS cc_start: 0.7584 (mttp) cc_final: 0.7170 (mttp) REVERT: E 128 ARG cc_start: 0.8425 (ptt180) cc_final: 0.8067 (ptt90) REVERT: E 153 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8196 (mm110) REVERT: E 191 ARG cc_start: 0.7432 (tpt90) cc_final: 0.7216 (tpm170) REVERT: E 301 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8538 (mm110) REVERT: E 302 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8106 (mtp85) REVERT: E 340 LEU cc_start: 0.8175 (mt) cc_final: 0.7673 (mt) REVERT: F 21 TYR cc_start: 0.8564 (m-80) cc_final: 0.8354 (m-80) REVERT: F 127 ILE cc_start: 0.8720 (mt) cc_final: 0.8277 (tt) REVERT: F 184 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7788 (tpm170) REVERT: F 201 GLU cc_start: 0.7300 (pm20) cc_final: 0.7090 (pm20) REVERT: F 226 GLN cc_start: 0.8108 (mt0) cc_final: 0.7718 (tt0) REVERT: F 231 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: F 256 GLU cc_start: 0.8063 (tt0) cc_final: 0.7839 (tt0) REVERT: F 364 ASP cc_start: 0.7938 (m-30) cc_final: 0.7694 (m-30) outliers start: 42 outliers final: 10 residues processed: 471 average time/residue: 0.7423 time to fit residues: 396.7706 Evaluate side-chains 359 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 346 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 231 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 225 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 172 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 317 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 295 HIS G 181 ASN ** G 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN H 295 HIS ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.171693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.131573 restraints weight = 28462.829| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.90 r_work: 0.3017 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 28236 Z= 0.252 Angle : 0.683 8.865 38228 Z= 0.351 Chirality : 0.048 0.261 4088 Planarity : 0.006 0.060 4992 Dihedral : 5.282 22.126 3812 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.14 % Allowed : 15.72 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.14), residues: 3468 helix: 0.44 (0.13), residues: 1460 sheet: -0.98 (0.22), residues: 456 loop : -1.65 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 292 TYR 0.011 0.002 TYR D 77 PHE 0.030 0.003 PHE G 342 TRP 0.010 0.001 TRP B 382 HIS 0.010 0.002 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00605 (28232) covalent geometry : angle 0.68261 (38220) SS BOND : bond 0.00580 ( 4) SS BOND : angle 2.10501 ( 8) hydrogen bonds : bond 0.04740 ( 1272) hydrogen bonds : angle 5.37095 ( 3576) *********************** REFINEMENT MACRO_CYCLE 3 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 440 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 379 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6513 (p0) cc_final: 0.6029 (t70) REVERT: A 74 MET cc_start: 0.6205 (ttm) cc_final: 0.5798 (mpt) REVERT: A 78 LYS cc_start: 0.7457 (mttp) cc_final: 0.7216 (ptpp) REVERT: A 80 LYS cc_start: 0.7761 (mttp) cc_final: 0.7019 (mttp) REVERT: A 128 ARG cc_start: 0.8399 (ptt180) cc_final: 0.8058 (ptt90) REVERT: A 191 ARG cc_start: 0.7418 (tpt90) cc_final: 0.7157 (tpm170) REVERT: A 302 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8049 (mtp85) REVERT: A 340 LEU cc_start: 0.8102 (mt) cc_final: 0.7631 (mt) REVERT: B 21 TYR cc_start: 0.8638 (m-80) cc_final: 0.8411 (m-80) REVERT: B 166 MET cc_start: 0.8265 (mtt) cc_final: 0.8045 (mtm) REVERT: B 184 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.7840 (tpm170) REVERT: B 201 GLU cc_start: 0.7737 (pm20) cc_final: 0.7490 (pm20) REVERT: B 226 GLN cc_start: 0.8158 (mt0) cc_final: 0.7776 (tt0) REVERT: B 364 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: C 25 ASP cc_start: 0.6528 (p0) cc_final: 0.5889 (t70) REVERT: C 74 MET cc_start: 0.6329 (ttm) cc_final: 0.5911 (mpt) REVERT: C 78 LYS cc_start: 0.7458 (mttp) cc_final: 0.7208 (ptpp) REVERT: C 80 LYS cc_start: 0.7719 (mttp) cc_final: 0.6987 (mttp) REVERT: C 128 ARG cc_start: 0.8407 (ptt180) cc_final: 0.8071 (ptt90) REVERT: C 153 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8255 (mm110) REVERT: C 191 ARG cc_start: 0.7392 (tpt90) cc_final: 0.7117 (tpm170) REVERT: C 302 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8114 (mmm-85) REVERT: C 340 LEU cc_start: 0.8127 (mt) cc_final: 0.7652 (mt) REVERT: C 393 ASP cc_start: 0.7761 (p0) cc_final: 0.7507 (p0) REVERT: D 21 TYR cc_start: 0.8607 (m-80) cc_final: 0.8379 (m-80) REVERT: D 76 ARG cc_start: 0.7610 (ptm160) cc_final: 0.7396 (ptm160) REVERT: D 127 ILE cc_start: 0.8681 (mt) cc_final: 0.8228 (tt) REVERT: D 184 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7838 (tpm170) REVERT: D 201 GLU cc_start: 0.7732 (pm20) cc_final: 0.7484 (pm20) REVERT: D 364 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: G 25 ASP cc_start: 0.6506 (p0) cc_final: 0.5873 (t70) REVERT: G 74 MET cc_start: 0.6334 (ttm) cc_final: 0.5924 (mpt) REVERT: G 78 LYS cc_start: 0.7520 (mttp) cc_final: 0.7269 (ptpp) REVERT: G 80 LYS cc_start: 0.7725 (mttp) cc_final: 0.6981 (mttp) REVERT: G 128 ARG cc_start: 0.8409 (ptt180) cc_final: 0.8071 (ptt90) REVERT: G 191 ARG cc_start: 0.7420 (tpt90) cc_final: 0.7188 (tpm170) REVERT: G 302 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8075 (mtp85) REVERT: G 340 LEU cc_start: 0.8091 (mt) cc_final: 0.7610 (mt) REVERT: H 21 TYR cc_start: 0.8627 (m-80) cc_final: 0.8414 (m-80) REVERT: H 127 ILE cc_start: 0.8666 (mt) cc_final: 0.8204 (tt) REVERT: H 184 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7829 (tpm170) REVERT: H 201 GLU cc_start: 0.7740 (pm20) cc_final: 0.7500 (pm20) REVERT: H 231 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: H 364 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: E 25 ASP cc_start: 0.6556 (p0) cc_final: 0.5933 (t70) REVERT: E 74 MET cc_start: 0.6193 (ttm) cc_final: 0.5809 (mpt) REVERT: E 78 LYS cc_start: 0.7450 (mttp) cc_final: 0.7208 (ptpp) REVERT: E 80 LYS cc_start: 0.7721 (mttp) cc_final: 0.6996 (mttp) REVERT: E 128 ARG cc_start: 0.8394 (ptt180) cc_final: 0.8056 (ptt90) REVERT: E 191 ARG cc_start: 0.7413 (tpt90) cc_final: 0.7141 (tpm170) REVERT: E 302 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8090 (mtp85) REVERT: E 340 LEU cc_start: 0.8110 (mt) cc_final: 0.7637 (mt) REVERT: F 21 TYR cc_start: 0.8642 (m-80) cc_final: 0.8409 (m-80) REVERT: F 76 ARG cc_start: 0.7602 (ptm160) cc_final: 0.7400 (ptm160) REVERT: F 127 ILE cc_start: 0.8662 (mt) cc_final: 0.8204 (tt) REVERT: F 184 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7842 (tpm170) REVERT: F 201 GLU cc_start: 0.7722 (pm20) cc_final: 0.7477 (pm20) REVERT: F 226 GLN cc_start: 0.8158 (mt0) cc_final: 0.7776 (tt0) REVERT: F 364 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7708 (m-30) outliers start: 61 outliers final: 19 residues processed: 402 average time/residue: 0.7586 time to fit residues: 346.8044 Evaluate side-chains 360 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 336 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 364 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 115 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 chunk 311 optimal weight: 0.0270 chunk 243 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 326 optimal weight: 2.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN B 92 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN D 92 ASN G 398 GLN H 92 ASN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.174041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.133695 restraints weight = 28062.539| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.91 r_work: 0.3034 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 28236 Z= 0.186 Angle : 0.623 7.622 38228 Z= 0.320 Chirality : 0.046 0.270 4088 Planarity : 0.005 0.049 4992 Dihedral : 5.061 21.501 3812 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.52 % Allowed : 16.60 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.14), residues: 3468 helix: 0.79 (0.13), residues: 1484 sheet: -0.84 (0.22), residues: 452 loop : -1.52 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 292 TYR 0.013 0.001 TYR E 187 PHE 0.029 0.002 PHE G 342 TRP 0.011 0.001 TRP D 382 HIS 0.007 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00443 (28232) covalent geometry : angle 0.62259 (38220) SS BOND : bond 0.00227 ( 4) SS BOND : angle 1.36171 ( 8) hydrogen bonds : bond 0.04134 ( 1272) hydrogen bonds : angle 5.10971 ( 3576) *********************** REFINEMENT MACRO_CYCLE 4 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 457 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 385 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6476 (p0) cc_final: 0.5817 (t70) REVERT: A 74 MET cc_start: 0.6351 (ttm) cc_final: 0.5931 (mpt) REVERT: A 80 LYS cc_start: 0.7700 (mttp) cc_final: 0.7042 (mttp) REVERT: A 128 ARG cc_start: 0.8418 (ptt180) cc_final: 0.8112 (ptt90) REVERT: A 191 ARG cc_start: 0.7410 (tpt90) cc_final: 0.7130 (tpm170) REVERT: A 302 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8167 (mmm-85) REVERT: A 340 LEU cc_start: 0.8160 (mt) cc_final: 0.7716 (mt) REVERT: B 127 ILE cc_start: 0.8656 (mt) cc_final: 0.8193 (tt) REVERT: B 166 MET cc_start: 0.8198 (mtt) cc_final: 0.7945 (mtm) REVERT: B 184 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7852 (tpm170) REVERT: B 201 GLU cc_start: 0.7805 (pm20) cc_final: 0.7569 (pm20) REVERT: B 364 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: C 25 ASP cc_start: 0.6486 (p0) cc_final: 0.5827 (t70) REVERT: C 74 MET cc_start: 0.6481 (ttm) cc_final: 0.6070 (mpt) REVERT: C 80 LYS cc_start: 0.7683 (mttp) cc_final: 0.7036 (mttp) REVERT: C 128 ARG cc_start: 0.8407 (ptt180) cc_final: 0.8108 (ptt90) REVERT: C 153 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8246 (mm110) REVERT: C 191 ARG cc_start: 0.7395 (tpt90) cc_final: 0.7112 (tpm170) REVERT: C 302 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8167 (mmm-85) REVERT: C 340 LEU cc_start: 0.8184 (mt) cc_final: 0.7719 (mt) REVERT: C 393 ASP cc_start: 0.7629 (p0) cc_final: 0.7305 (p0) REVERT: D 127 ILE cc_start: 0.8661 (mt) cc_final: 0.8226 (tt) REVERT: D 184 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.7891 (tpm170) REVERT: D 201 GLU cc_start: 0.7805 (pm20) cc_final: 0.7569 (pm20) REVERT: D 364 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: G 25 ASP cc_start: 0.6458 (p0) cc_final: 0.5816 (t70) REVERT: G 74 MET cc_start: 0.6426 (ttm) cc_final: 0.6057 (mpt) REVERT: G 80 LYS cc_start: 0.7686 (mttp) cc_final: 0.7016 (mttp) REVERT: G 128 ARG cc_start: 0.8424 (ptt180) cc_final: 0.8115 (ptt90) REVERT: G 302 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8176 (mmm-85) REVERT: G 340 LEU cc_start: 0.8182 (mt) cc_final: 0.7729 (mt) REVERT: H 21 TYR cc_start: 0.8632 (m-80) cc_final: 0.8407 (m-80) REVERT: H 127 ILE cc_start: 0.8647 (mt) cc_final: 0.8204 (tt) REVERT: H 184 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.7880 (tpm170) REVERT: H 201 GLU cc_start: 0.7810 (pm20) cc_final: 0.7579 (pm20) REVERT: H 364 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: E 25 ASP cc_start: 0.6472 (p0) cc_final: 0.5832 (t70) REVERT: E 74 MET cc_start: 0.6344 (ttm) cc_final: 0.5917 (mpt) REVERT: E 80 LYS cc_start: 0.7690 (mttp) cc_final: 0.7041 (mttp) REVERT: E 128 ARG cc_start: 0.8422 (ptt180) cc_final: 0.8114 (ptt90) REVERT: E 191 ARG cc_start: 0.7421 (tpt90) cc_final: 0.7128 (tpm170) REVERT: E 302 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8157 (mmm-85) REVERT: E 340 LEU cc_start: 0.8163 (mt) cc_final: 0.7761 (mt) REVERT: F 127 ILE cc_start: 0.8658 (mt) cc_final: 0.8222 (tt) REVERT: F 184 ARG cc_start: 0.8291 (mmm-85) cc_final: 0.7868 (tpm170) REVERT: F 201 GLU cc_start: 0.7807 (pm20) cc_final: 0.7569 (pm20) REVERT: F 364 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7769 (m-30) outliers start: 72 outliers final: 21 residues processed: 418 average time/residue: 0.7852 time to fit residues: 375.9373 Evaluate side-chains 382 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 357 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain D residue 189 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain E residue 189 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 323 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 305 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 233 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 209 GLN D 398 GLN ** G 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN ** H 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 GLN F 209 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.171219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.129631 restraints weight = 28104.608| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.00 r_work: 0.2982 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 28236 Z= 0.354 Angle : 0.758 9.757 38228 Z= 0.389 Chirality : 0.053 0.305 4088 Planarity : 0.006 0.077 4992 Dihedral : 5.474 21.532 3812 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.98 % Allowed : 18.49 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3468 helix: 0.40 (0.13), residues: 1468 sheet: -1.04 (0.21), residues: 476 loop : -1.56 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 212 TYR 0.015 0.002 TYR G 17 PHE 0.031 0.003 PHE A 342 TRP 0.014 0.002 TRP D 382 HIS 0.010 0.002 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00855 (28232) covalent geometry : angle 0.75781 (38220) SS BOND : bond 0.00828 ( 4) SS BOND : angle 2.30717 ( 8) hydrogen bonds : bond 0.05131 ( 1272) hydrogen bonds : angle 5.47985 ( 3576) *********************** REFINEMENT MACRO_CYCLE 5 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 420 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 335 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6439 (p0) cc_final: 0.5796 (t70) REVERT: A 74 MET cc_start: 0.6311 (ttm) cc_final: 0.5804 (mpt) REVERT: A 80 LYS cc_start: 0.7866 (mttp) cc_final: 0.7103 (mttp) REVERT: A 128 ARG cc_start: 0.8391 (ptt180) cc_final: 0.8119 (ptt90) REVERT: A 184 ARG cc_start: 0.8655 (tpm170) cc_final: 0.8293 (tpm170) REVERT: A 191 ARG cc_start: 0.7519 (tpt90) cc_final: 0.7148 (tpm170) REVERT: A 301 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8760 (mm-40) REVERT: A 302 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8112 (mtp85) REVERT: A 340 LEU cc_start: 0.8154 (mt) cc_final: 0.7799 (mt) REVERT: B 127 ILE cc_start: 0.8701 (mt) cc_final: 0.8254 (tt) REVERT: B 155 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: B 180 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7610 (ttpp) REVERT: B 184 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.7885 (tpm170) REVERT: B 194 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7792 (mt) REVERT: B 201 GLU cc_start: 0.7845 (pm20) cc_final: 0.7457 (pm20) REVERT: B 364 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: C 25 ASP cc_start: 0.6461 (p0) cc_final: 0.5798 (t70) REVERT: C 74 MET cc_start: 0.6487 (ttm) cc_final: 0.5981 (mpt) REVERT: C 80 LYS cc_start: 0.7865 (mttp) cc_final: 0.7104 (mttp) REVERT: C 128 ARG cc_start: 0.8391 (ptt180) cc_final: 0.8121 (ptt90) REVERT: C 153 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8243 (mm110) REVERT: C 184 ARG cc_start: 0.8663 (tpm170) cc_final: 0.8297 (tpm170) REVERT: C 301 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8757 (mm-40) REVERT: C 302 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8099 (mtp85) REVERT: C 340 LEU cc_start: 0.8171 (mt) cc_final: 0.7807 (mt) REVERT: D 127 ILE cc_start: 0.8665 (mt) cc_final: 0.8246 (tt) REVERT: D 155 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: D 166 MET cc_start: 0.8733 (mtm) cc_final: 0.8530 (mtm) REVERT: D 184 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.7881 (tpm170) REVERT: D 194 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7775 (mt) REVERT: D 201 GLU cc_start: 0.7822 (pm20) cc_final: 0.7423 (pm20) REVERT: D 364 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: G 25 ASP cc_start: 0.6427 (p0) cc_final: 0.5788 (t70) REVERT: G 74 MET cc_start: 0.6502 (ttm) cc_final: 0.5984 (mpt) REVERT: G 80 LYS cc_start: 0.7865 (mttp) cc_final: 0.7107 (mttp) REVERT: G 128 ARG cc_start: 0.8370 (ptt180) cc_final: 0.8120 (ptt90) REVERT: G 301 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8761 (mm-40) REVERT: G 302 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8115 (mtp85) REVERT: G 340 LEU cc_start: 0.8161 (mt) cc_final: 0.7806 (mt) REVERT: H 127 ILE cc_start: 0.8687 (mt) cc_final: 0.8248 (tt) REVERT: H 155 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: H 184 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.7882 (tpm170) REVERT: H 194 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7731 (mt) REVERT: H 201 GLU cc_start: 0.7839 (pm20) cc_final: 0.7451 (pm20) REVERT: H 279 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8877 (mttm) REVERT: H 364 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: E 25 ASP cc_start: 0.6427 (p0) cc_final: 0.5805 (t70) REVERT: E 74 MET cc_start: 0.6336 (ttm) cc_final: 0.5818 (mpt) REVERT: E 80 LYS cc_start: 0.7876 (mttp) cc_final: 0.7118 (mttp) REVERT: E 128 ARG cc_start: 0.8368 (ptt180) cc_final: 0.8101 (ptt90) REVERT: E 184 ARG cc_start: 0.8642 (tpm170) cc_final: 0.8277 (tpm170) REVERT: E 301 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8744 (mm-40) REVERT: E 302 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8090 (mtp85) REVERT: E 340 LEU cc_start: 0.8157 (mt) cc_final: 0.7794 (mt) REVERT: F 127 ILE cc_start: 0.8690 (mt) cc_final: 0.8264 (tt) REVERT: F 155 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: F 184 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7864 (tpm170) REVERT: F 201 GLU cc_start: 0.7841 (pm20) cc_final: 0.7443 (pm20) REVERT: F 364 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7895 (m-30) outliers start: 85 outliers final: 44 residues processed: 391 average time/residue: 0.7551 time to fit residues: 340.4999 Evaluate side-chains 372 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 189 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 189 CYS Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 279 LYS Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 189 CYS Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 189 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 328 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 296 optimal weight: 0.6980 chunk 334 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 339 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 398 GLN H 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.175655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.134778 restraints weight = 27989.410| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.83 r_work: 0.3100 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 28236 Z= 0.121 Angle : 0.578 9.455 38228 Z= 0.298 Chirality : 0.044 0.292 4088 Planarity : 0.005 0.041 4992 Dihedral : 4.833 21.501 3812 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.14 % Allowed : 19.75 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.14), residues: 3468 helix: 1.13 (0.13), residues: 1488 sheet: -0.93 (0.22), residues: 472 loop : -1.35 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 302 TYR 0.015 0.001 TYR B 26 PHE 0.028 0.002 PHE G 342 TRP 0.010 0.001 TRP F 382 HIS 0.004 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00275 (28232) covalent geometry : angle 0.57818 (38220) SS BOND : bond 0.00155 ( 4) SS BOND : angle 1.14250 ( 8) hydrogen bonds : bond 0.03577 ( 1272) hydrogen bonds : angle 4.94959 ( 3576) *********************** REFINEMENT MACRO_CYCLE 6 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 460 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 399 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6256 (p0) cc_final: 0.5849 (t70) REVERT: A 74 MET cc_start: 0.6043 (ttm) cc_final: 0.5662 (mpt) REVERT: A 80 LYS cc_start: 0.7731 (mttp) cc_final: 0.7099 (mttp) REVERT: A 128 ARG cc_start: 0.8356 (ptt180) cc_final: 0.8096 (ptt90) REVERT: A 184 ARG cc_start: 0.8552 (tpm170) cc_final: 0.8164 (tpm170) REVERT: A 302 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: A 340 LEU cc_start: 0.8150 (mt) cc_final: 0.7775 (mt) REVERT: A 426 GLN cc_start: 0.6308 (tt0) cc_final: 0.6105 (tt0) REVERT: B 21 TYR cc_start: 0.8529 (m-80) cc_final: 0.8240 (m-80) REVERT: B 127 ILE cc_start: 0.8601 (mt) cc_final: 0.8170 (tt) REVERT: B 184 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7869 (tpm170) REVERT: B 201 GLU cc_start: 0.7785 (pm20) cc_final: 0.7285 (pm20) REVERT: B 364 ASP cc_start: 0.7880 (m-30) cc_final: 0.7646 (m-30) REVERT: C 25 ASP cc_start: 0.6255 (p0) cc_final: 0.5839 (t70) REVERT: C 74 MET cc_start: 0.6112 (ttm) cc_final: 0.5731 (mpt) REVERT: C 80 LYS cc_start: 0.7740 (mttp) cc_final: 0.7106 (mttp) REVERT: C 128 ARG cc_start: 0.8348 (ptt180) cc_final: 0.8082 (ptt90) REVERT: C 184 ARG cc_start: 0.8549 (tpm170) cc_final: 0.8165 (tpm170) REVERT: C 248 MET cc_start: 0.9035 (mmp) cc_final: 0.8784 (mmp) REVERT: C 302 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.7998 (mmm-85) REVERT: C 340 LEU cc_start: 0.8106 (mt) cc_final: 0.7724 (mt) REVERT: D 21 TYR cc_start: 0.8546 (m-80) cc_final: 0.8264 (m-80) REVERT: D 127 ILE cc_start: 0.8663 (mt) cc_final: 0.8150 (tt) REVERT: D 184 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7875 (tpm170) REVERT: D 201 GLU cc_start: 0.7793 (pm20) cc_final: 0.7403 (pm20) REVERT: D 364 ASP cc_start: 0.7957 (m-30) cc_final: 0.7748 (m-30) REVERT: D 398 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7974 (tp40) REVERT: G 25 ASP cc_start: 0.6234 (p0) cc_final: 0.5838 (t70) REVERT: G 74 MET cc_start: 0.6147 (ttm) cc_final: 0.5709 (mpt) REVERT: G 80 LYS cc_start: 0.7713 (mttp) cc_final: 0.7078 (mttp) REVERT: G 128 ARG cc_start: 0.8357 (ptt180) cc_final: 0.8105 (ptt90) REVERT: G 169 CYS cc_start: 0.8001 (t) cc_final: 0.7770 (p) REVERT: G 302 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.7998 (mmm-85) REVERT: G 340 LEU cc_start: 0.8134 (mt) cc_final: 0.7753 (mt) REVERT: G 426 GLN cc_start: 0.6308 (tt0) cc_final: 0.6098 (tt0) REVERT: H 21 TYR cc_start: 0.8587 (m-80) cc_final: 0.8332 (m-80) REVERT: H 127 ILE cc_start: 0.8618 (mt) cc_final: 0.8136 (tt) REVERT: H 184 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.7888 (tpm170) REVERT: H 201 GLU cc_start: 0.7796 (pm20) cc_final: 0.7288 (pm20) REVERT: H 335 ASP cc_start: 0.5125 (OUTLIER) cc_final: 0.4906 (t0) REVERT: H 364 ASP cc_start: 0.7901 (m-30) cc_final: 0.7694 (m-30) REVERT: H 398 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7970 (tp40) REVERT: E 25 ASP cc_start: 0.6256 (p0) cc_final: 0.5859 (t70) REVERT: E 74 MET cc_start: 0.6103 (ttm) cc_final: 0.5686 (mpt) REVERT: E 80 LYS cc_start: 0.7729 (mttp) cc_final: 0.7102 (mttp) REVERT: E 128 ARG cc_start: 0.8342 (ptt180) cc_final: 0.8087 (ptt90) REVERT: E 184 ARG cc_start: 0.8537 (tpm170) cc_final: 0.8150 (tpm170) REVERT: E 302 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.7966 (mmm-85) REVERT: E 340 LEU cc_start: 0.8121 (mt) cc_final: 0.7733 (mt) REVERT: F 21 TYR cc_start: 0.8536 (m-80) cc_final: 0.8252 (m-80) REVERT: F 127 ILE cc_start: 0.8620 (mt) cc_final: 0.8151 (tt) REVERT: F 184 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7884 (tpm170) REVERT: F 201 GLU cc_start: 0.7803 (pm20) cc_final: 0.7300 (pm20) REVERT: F 364 ASP cc_start: 0.7903 (m-30) cc_final: 0.7667 (m-30) outliers start: 61 outliers final: 32 residues processed: 439 average time/residue: 0.7821 time to fit residues: 393.9567 Evaluate side-chains 389 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 354 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain D residue 189 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 398 GLN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain H residue 189 CYS Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 298 ILE Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 398 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 189 CYS Chi-restraints excluded: chain F residue 189 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 153 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 347 optimal weight: 0.0060 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN B 209 GLN B 301 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 GLN D 92 ASN D 209 GLN D 301 GLN D 398 GLN G 226 GLN H 92 ASN H 209 GLN H 301 GLN H 398 GLN E 226 GLN F 92 ASN F 209 GLN F 301 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.172160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.131840 restraints weight = 28050.659| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.91 r_work: 0.3023 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28236 Z= 0.225 Angle : 0.656 8.600 38228 Z= 0.336 Chirality : 0.048 0.316 4088 Planarity : 0.005 0.056 4992 Dihedral : 5.063 21.817 3812 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.03 % Allowed : 21.92 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.14), residues: 3468 helix: 1.06 (0.13), residues: 1460 sheet: -0.99 (0.22), residues: 476 loop : -1.33 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.013 0.002 TYR G 26 PHE 0.028 0.002 PHE C 342 TRP 0.012 0.001 TRP F 382 HIS 0.008 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00540 (28232) covalent geometry : angle 0.65573 (38220) SS BOND : bond 0.00505 ( 4) SS BOND : angle 1.57966 ( 8) hydrogen bonds : bond 0.04313 ( 1272) hydrogen bonds : angle 5.10371 ( 3576) *********************** REFINEMENT MACRO_CYCLE 7 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 407 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 349 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6292 (p0) cc_final: 0.5751 (t70) REVERT: A 74 MET cc_start: 0.6011 (ttm) cc_final: 0.5596 (mpt) REVERT: A 80 LYS cc_start: 0.7762 (mttp) cc_final: 0.7029 (mttp) REVERT: A 128 ARG cc_start: 0.8275 (ptt180) cc_final: 0.8019 (ptt90) REVERT: A 184 ARG cc_start: 0.8628 (tpm170) cc_final: 0.8009 (tpm170) REVERT: A 302 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.8089 (mmm-85) REVERT: A 340 LEU cc_start: 0.8094 (mt) cc_final: 0.7720 (mt) REVERT: B 21 TYR cc_start: 0.8544 (m-80) cc_final: 0.8241 (m-80) REVERT: B 127 ILE cc_start: 0.8621 (mt) cc_final: 0.8154 (tt) REVERT: B 155 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: B 184 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7808 (tpm170) REVERT: B 201 GLU cc_start: 0.7821 (pm20) cc_final: 0.7600 (pm20) REVERT: B 364 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: C 25 ASP cc_start: 0.6343 (p0) cc_final: 0.5785 (t70) REVERT: C 74 MET cc_start: 0.6034 (ttm) cc_final: 0.5623 (mpt) REVERT: C 80 LYS cc_start: 0.7782 (mttp) cc_final: 0.7038 (mttp) REVERT: C 128 ARG cc_start: 0.8262 (ptt180) cc_final: 0.8006 (ptt90) REVERT: C 184 ARG cc_start: 0.8632 (tpm170) cc_final: 0.8018 (tpm170) REVERT: C 302 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.7981 (mmm-85) REVERT: C 340 LEU cc_start: 0.8076 (mt) cc_final: 0.7694 (mt) REVERT: D 21 TYR cc_start: 0.8548 (m-80) cc_final: 0.8244 (m-80) REVERT: D 127 ILE cc_start: 0.8642 (mt) cc_final: 0.8172 (tt) REVERT: D 184 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7809 (tpm170) REVERT: D 201 GLU cc_start: 0.7841 (pm20) cc_final: 0.7615 (pm20) REVERT: D 364 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: G 25 ASP cc_start: 0.6304 (p0) cc_final: 0.5772 (t70) REVERT: G 74 MET cc_start: 0.6024 (ttm) cc_final: 0.5606 (mpt) REVERT: G 80 LYS cc_start: 0.7767 (mttp) cc_final: 0.7027 (mttp) REVERT: G 128 ARG cc_start: 0.8255 (ptt180) cc_final: 0.8015 (ptt90) REVERT: G 302 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8009 (mmm-85) REVERT: G 340 LEU cc_start: 0.8076 (mt) cc_final: 0.7694 (mt) REVERT: G 352 GLU cc_start: 0.8156 (mp0) cc_final: 0.7898 (mp0) REVERT: H 21 TYR cc_start: 0.8551 (m-80) cc_final: 0.8333 (m-80) REVERT: H 125 LYS cc_start: 0.8636 (mmtm) cc_final: 0.7813 (mmtt) REVERT: H 127 ILE cc_start: 0.8663 (mt) cc_final: 0.8140 (tt) REVERT: H 184 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7794 (tpm170) REVERT: H 201 GLU cc_start: 0.7832 (pm20) cc_final: 0.7613 (pm20) REVERT: H 364 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: E 25 ASP cc_start: 0.6342 (p0) cc_final: 0.5795 (t70) REVERT: E 74 MET cc_start: 0.5998 (ttm) cc_final: 0.5584 (mpt) REVERT: E 80 LYS cc_start: 0.7770 (mttp) cc_final: 0.7036 (mttp) REVERT: E 128 ARG cc_start: 0.8324 (ptt180) cc_final: 0.8071 (ptt90) REVERT: E 184 ARG cc_start: 0.8646 (tpm170) cc_final: 0.8026 (tpm170) REVERT: E 201 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6962 (pt0) REVERT: E 302 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: E 340 LEU cc_start: 0.8067 (mt) cc_final: 0.7685 (mt) REVERT: E 352 GLU cc_start: 0.8145 (mp0) cc_final: 0.7885 (mp0) REVERT: F 21 TYR cc_start: 0.8550 (m-80) cc_final: 0.8247 (m-80) REVERT: F 125 LYS cc_start: 0.8649 (mmtm) cc_final: 0.7816 (mmtt) REVERT: F 127 ILE cc_start: 0.8637 (mt) cc_final: 0.8146 (tt) REVERT: F 184 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.7803 (tpm170) REVERT: F 201 GLU cc_start: 0.7841 (pm20) cc_final: 0.7614 (pm20) REVERT: F 364 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7851 (m-30) outliers start: 58 outliers final: 37 residues processed: 385 average time/residue: 0.6934 time to fit residues: 307.6339 Evaluate side-chains 383 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 340 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain D residue 189 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain H residue 189 CYS Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 189 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 265 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN B 380 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 380 HIS G 226 GLN H 92 ASN H 380 HIS F 92 ASN F 380 HIS ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.173470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.134612 restraints weight = 28146.970| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.95 r_work: 0.3050 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28236 Z= 0.176 Angle : 0.623 10.021 38228 Z= 0.319 Chirality : 0.046 0.326 4088 Planarity : 0.005 0.046 4992 Dihedral : 4.953 21.472 3812 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.10 % Allowed : 22.34 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.14), residues: 3468 helix: 1.20 (0.13), residues: 1460 sheet: -0.93 (0.22), residues: 472 loop : -1.32 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.012 0.001 TYR F 77 PHE 0.027 0.002 PHE C 342 TRP 0.011 0.001 TRP F 382 HIS 0.006 0.001 HIS H 150 Details of bonding type rmsd covalent geometry : bond 0.00418 (28232) covalent geometry : angle 0.62239 (38220) SS BOND : bond 0.00310 ( 4) SS BOND : angle 1.42344 ( 8) hydrogen bonds : bond 0.04002 ( 1272) hydrogen bonds : angle 5.01586 ( 3576) *********************** REFINEMENT MACRO_CYCLE 8 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 413 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 353 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6223 (p0) cc_final: 0.5778 (t70) REVERT: A 80 LYS cc_start: 0.7720 (mttp) cc_final: 0.7073 (mttp) REVERT: A 302 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7903 (mmm-85) REVERT: A 340 LEU cc_start: 0.8151 (mt) cc_final: 0.7789 (mt) REVERT: B 21 TYR cc_start: 0.8603 (m-80) cc_final: 0.8269 (m-80) REVERT: B 125 LYS cc_start: 0.8670 (mmtm) cc_final: 0.7789 (mmtt) REVERT: B 127 ILE cc_start: 0.8647 (mt) cc_final: 0.8263 (tt) REVERT: B 184 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7875 (tpm170) REVERT: B 201 GLU cc_start: 0.7818 (pm20) cc_final: 0.7411 (pm20) REVERT: B 364 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: C 25 ASP cc_start: 0.6232 (p0) cc_final: 0.5779 (t70) REVERT: C 80 LYS cc_start: 0.7698 (mttp) cc_final: 0.7070 (mttp) REVERT: C 302 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.7895 (mmm-85) REVERT: C 340 LEU cc_start: 0.8158 (mt) cc_final: 0.7790 (mt) REVERT: D 21 TYR cc_start: 0.8581 (m-80) cc_final: 0.8247 (m-80) REVERT: D 125 LYS cc_start: 0.8693 (mmtm) cc_final: 0.7831 (mmtt) REVERT: D 127 ILE cc_start: 0.8682 (mt) cc_final: 0.8269 (tt) REVERT: D 184 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7895 (tpm170) REVERT: D 201 GLU cc_start: 0.7827 (pm20) cc_final: 0.7424 (pm20) REVERT: D 364 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: G 25 ASP cc_start: 0.6195 (p0) cc_final: 0.5776 (t70) REVERT: G 80 LYS cc_start: 0.7690 (mttp) cc_final: 0.7060 (mttp) REVERT: G 302 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: G 340 LEU cc_start: 0.8156 (mt) cc_final: 0.7788 (mt) REVERT: H 21 TYR cc_start: 0.8592 (m-80) cc_final: 0.8379 (m-80) REVERT: H 125 LYS cc_start: 0.8687 (mmtm) cc_final: 0.7809 (mmtt) REVERT: H 127 ILE cc_start: 0.8697 (mt) cc_final: 0.8244 (tt) REVERT: H 184 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7900 (tpm170) REVERT: H 201 GLU cc_start: 0.7823 (pm20) cc_final: 0.7427 (pm20) REVERT: H 364 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7694 (m-30) REVERT: E 25 ASP cc_start: 0.6211 (p0) cc_final: 0.5791 (t70) REVERT: E 80 LYS cc_start: 0.7713 (mttp) cc_final: 0.7083 (mttp) REVERT: E 201 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6984 (pt0) REVERT: E 302 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7879 (mmm-85) REVERT: E 340 LEU cc_start: 0.8148 (mt) cc_final: 0.7779 (mt) REVERT: F 21 TYR cc_start: 0.8577 (m-80) cc_final: 0.8242 (m-80) REVERT: F 125 LYS cc_start: 0.8676 (mmtm) cc_final: 0.7791 (mmtt) REVERT: F 127 ILE cc_start: 0.8687 (mt) cc_final: 0.8246 (tt) REVERT: F 184 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7899 (tpm170) REVERT: F 201 GLU cc_start: 0.7816 (pm20) cc_final: 0.7397 (pm20) REVERT: F 364 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7724 (m-30) outliers start: 60 outliers final: 34 residues processed: 386 average time/residue: 0.8003 time to fit residues: 354.8987 Evaluate side-chains 385 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 346 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 189 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain H residue 189 CYS Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 298 ILE Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 189 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 381 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 67 optimal weight: 0.8980 chunk 323 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 344 optimal weight: 30.0000 chunk 259 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN C 398 GLN D 92 ASN G 226 GLN H 92 ASN F 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.177077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.135968 restraints weight = 28009.019| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.94 r_work: 0.3119 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28236 Z= 0.112 Angle : 0.567 11.357 38228 Z= 0.291 Chirality : 0.043 0.317 4088 Planarity : 0.005 0.049 4992 Dihedral : 4.684 22.138 3812 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.26 % Allowed : 23.42 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.14), residues: 3468 helix: 1.50 (0.13), residues: 1488 sheet: -0.80 (0.22), residues: 452 loop : -1.28 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.019 0.001 TYR C 26 PHE 0.025 0.002 PHE A 342 TRP 0.011 0.001 TRP H 211 HIS 0.003 0.001 HIS G 289 Details of bonding type rmsd covalent geometry : bond 0.00253 (28232) covalent geometry : angle 0.56676 (38220) SS BOND : bond 0.00071 ( 4) SS BOND : angle 1.02282 ( 8) hydrogen bonds : bond 0.03384 ( 1272) hydrogen bonds : angle 4.77618 ( 3576) *********************** REFINEMENT MACRO_CYCLE 9 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 418 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 382 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6223 (p0) cc_final: 0.5615 (t70) REVERT: A 80 LYS cc_start: 0.7538 (mttp) cc_final: 0.6917 (mttp) REVERT: A 302 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7905 (mmm-85) REVERT: A 340 LEU cc_start: 0.7995 (mt) cc_final: 0.7576 (mt) REVERT: B 21 TYR cc_start: 0.8480 (m-80) cc_final: 0.8237 (m-80) REVERT: B 45 VAL cc_start: 0.7815 (m) cc_final: 0.7547 (p) REVERT: B 125 LYS cc_start: 0.8644 (mmtm) cc_final: 0.7725 (mmtt) REVERT: B 127 ILE cc_start: 0.8505 (mt) cc_final: 0.8152 (tt) REVERT: B 184 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7765 (tpm170) REVERT: B 201 GLU cc_start: 0.7588 (pm20) cc_final: 0.7265 (pm20) REVERT: B 364 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: B 398 GLN cc_start: 0.8307 (mm110) cc_final: 0.7866 (tp40) REVERT: C 25 ASP cc_start: 0.6229 (p0) cc_final: 0.5606 (t70) REVERT: C 80 LYS cc_start: 0.7546 (mttp) cc_final: 0.6925 (mttp) REVERT: C 302 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.7934 (mmm-85) REVERT: C 340 LEU cc_start: 0.7990 (mt) cc_final: 0.7569 (mt) REVERT: D 21 TYR cc_start: 0.8479 (m-80) cc_final: 0.8229 (m-80) REVERT: D 45 VAL cc_start: 0.7842 (m) cc_final: 0.7564 (p) REVERT: D 125 LYS cc_start: 0.8687 (mmtm) cc_final: 0.7769 (mmtt) REVERT: D 127 ILE cc_start: 0.8539 (mt) cc_final: 0.8129 (tt) REVERT: D 184 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7741 (tpm170) REVERT: D 201 GLU cc_start: 0.7614 (pm20) cc_final: 0.7290 (pm20) REVERT: G 25 ASP cc_start: 0.6212 (p0) cc_final: 0.5608 (t70) REVERT: G 80 LYS cc_start: 0.7530 (mttp) cc_final: 0.6901 (mttp) REVERT: G 169 CYS cc_start: 0.7867 (t) cc_final: 0.7599 (p) REVERT: G 302 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7934 (mmm-85) REVERT: G 340 LEU cc_start: 0.7988 (mt) cc_final: 0.7571 (mt) REVERT: H 45 VAL cc_start: 0.7819 (m) cc_final: 0.7541 (p) REVERT: H 125 LYS cc_start: 0.8669 (mmtm) cc_final: 0.7752 (mmtt) REVERT: H 127 ILE cc_start: 0.8555 (mt) cc_final: 0.8112 (tt) REVERT: H 184 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7781 (tpm170) REVERT: H 201 GLU cc_start: 0.7597 (pm20) cc_final: 0.7272 (pm20) REVERT: H 398 GLN cc_start: 0.8297 (mm110) cc_final: 0.7958 (tp40) REVERT: E 25 ASP cc_start: 0.6223 (p0) cc_final: 0.5631 (t70) REVERT: E 80 LYS cc_start: 0.7549 (mttp) cc_final: 0.6929 (mttp) REVERT: E 201 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: E 302 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7908 (mmm-85) REVERT: E 340 LEU cc_start: 0.7994 (mt) cc_final: 0.7572 (mt) REVERT: F 21 TYR cc_start: 0.8480 (m-80) cc_final: 0.8238 (m-80) REVERT: F 45 VAL cc_start: 0.7823 (m) cc_final: 0.7546 (p) REVERT: F 125 LYS cc_start: 0.8679 (mmtm) cc_final: 0.7774 (mmtt) REVERT: F 127 ILE cc_start: 0.8556 (mt) cc_final: 0.8130 (tt) REVERT: F 184 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7710 (tpm170) REVERT: F 201 GLU cc_start: 0.7585 (pm20) cc_final: 0.7257 (pm20) REVERT: F 364 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: F 398 GLN cc_start: 0.8310 (mm110) cc_final: 0.7859 (tp40) outliers start: 36 outliers final: 25 residues processed: 403 average time/residue: 0.7373 time to fit residues: 341.3600 Evaluate side-chains 375 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 347 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 189 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain H residue 189 CYS Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 189 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 7.9990 chunk 314 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 343 optimal weight: 3.9990 chunk 268 optimal weight: 0.0870 chunk 295 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 253 optimal weight: 10.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN B 92 ASN B 146 GLN C 226 GLN C 398 GLN D 92 ASN G 226 GLN G 398 GLN H 92 ASN E 226 GLN E 398 GLN F 92 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.172618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130562 restraints weight = 28048.134| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.89 r_work: 0.3041 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 28236 Z= 0.293 Angle : 0.718 9.672 38228 Z= 0.367 Chirality : 0.050 0.350 4088 Planarity : 0.006 0.062 4992 Dihedral : 5.152 21.104 3812 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.19 % Allowed : 24.19 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.14), residues: 3468 helix: 1.01 (0.13), residues: 1464 sheet: -0.99 (0.21), residues: 520 loop : -1.31 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 76 TYR 0.021 0.002 TYR C 26 PHE 0.029 0.003 PHE A 342 TRP 0.017 0.002 TRP H 382 HIS 0.008 0.002 HIS F 150 Details of bonding type rmsd covalent geometry : bond 0.00708 (28232) covalent geometry : angle 0.71721 (38220) SS BOND : bond 0.00698 ( 4) SS BOND : angle 2.05202 ( 8) hydrogen bonds : bond 0.04616 ( 1272) hydrogen bonds : angle 5.18087 ( 3576) ********************** REFINEMENT MACRO_CYCLE 10 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 374 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 340 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6320 (p0) cc_final: 0.5693 (t70) REVERT: A 80 LYS cc_start: 0.7803 (mttp) cc_final: 0.7118 (mttp) REVERT: A 184 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8296 (tpm170) REVERT: A 302 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.8042 (mmm-85) REVERT: A 340 LEU cc_start: 0.8168 (mt) cc_final: 0.7817 (mt) REVERT: B 45 VAL cc_start: 0.7831 (m) cc_final: 0.7569 (p) REVERT: B 125 LYS cc_start: 0.8675 (mmtm) cc_final: 0.7791 (mmtt) REVERT: B 127 ILE cc_start: 0.8613 (mt) cc_final: 0.8353 (tt) REVERT: B 184 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.7894 (tpm170) REVERT: B 201 GLU cc_start: 0.7743 (pm20) cc_final: 0.7509 (pm20) REVERT: B 346 MET cc_start: 0.8448 (ptm) cc_final: 0.7558 (ptm) REVERT: B 364 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: C 25 ASP cc_start: 0.6343 (p0) cc_final: 0.5690 (t70) REVERT: C 80 LYS cc_start: 0.7800 (mttp) cc_final: 0.7115 (mttp) REVERT: C 184 ARG cc_start: 0.8697 (tpp-160) cc_final: 0.8329 (tpm170) REVERT: C 302 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8022 (mmm-85) REVERT: C 340 LEU cc_start: 0.8152 (mt) cc_final: 0.7793 (mt) REVERT: D 45 VAL cc_start: 0.7863 (m) cc_final: 0.7587 (p) REVERT: D 127 ILE cc_start: 0.8681 (mt) cc_final: 0.8343 (tt) REVERT: D 184 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7910 (tpm170) REVERT: D 201 GLU cc_start: 0.7757 (pm20) cc_final: 0.7516 (pm20) REVERT: D 346 MET cc_start: 0.8462 (ptm) cc_final: 0.7578 (ptm) REVERT: G 25 ASP cc_start: 0.6311 (p0) cc_final: 0.5698 (t70) REVERT: G 80 LYS cc_start: 0.7788 (mttp) cc_final: 0.7109 (mttp) REVERT: G 302 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8040 (mmm-85) REVERT: G 340 LEU cc_start: 0.8165 (mt) cc_final: 0.7790 (mt) REVERT: H 45 VAL cc_start: 0.7831 (m) cc_final: 0.7561 (p) REVERT: H 127 ILE cc_start: 0.8660 (mt) cc_final: 0.8278 (tt) REVERT: H 184 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7906 (tpm170) REVERT: H 201 GLU cc_start: 0.7740 (pm20) cc_final: 0.7504 (pm20) REVERT: H 346 MET cc_start: 0.8482 (ptm) cc_final: 0.7592 (ptm) REVERT: E 25 ASP cc_start: 0.6315 (p0) cc_final: 0.5691 (t70) REVERT: E 80 LYS cc_start: 0.7811 (mttp) cc_final: 0.7131 (mttp) REVERT: E 184 ARG cc_start: 0.8683 (tpp-160) cc_final: 0.8313 (tpm170) REVERT: E 201 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: E 302 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8015 (mmm-85) REVERT: E 340 LEU cc_start: 0.8165 (mt) cc_final: 0.7782 (mt) REVERT: F 45 VAL cc_start: 0.7826 (m) cc_final: 0.7558 (p) REVERT: F 125 LYS cc_start: 0.8685 (mmtm) cc_final: 0.7793 (mmtt) REVERT: F 127 ILE cc_start: 0.8678 (mt) cc_final: 0.8321 (tt) REVERT: F 184 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7918 (tpm170) REVERT: F 201 GLU cc_start: 0.7752 (pm20) cc_final: 0.7513 (pm20) REVERT: F 346 MET cc_start: 0.8492 (ptm) cc_final: 0.7622 (ptm) REVERT: F 364 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7796 (m-30) outliers start: 34 outliers final: 30 residues processed: 361 average time/residue: 0.7528 time to fit residues: 311.3948 Evaluate side-chains 356 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 323 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 189 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain H residue 189 CYS Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 189 CYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 337 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN B 92 ASN B 204 ASN C 301 GLN D 92 ASN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 204 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.175786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.134118 restraints weight = 27878.944| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.96 r_work: 0.3102 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28236 Z= 0.119 Angle : 0.591 10.893 38228 Z= 0.302 Chirality : 0.044 0.323 4088 Planarity : 0.005 0.046 4992 Dihedral : 4.762 22.052 3812 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.09 % Allowed : 24.51 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.14), residues: 3468 helix: 1.39 (0.13), residues: 1488 sheet: -0.88 (0.22), residues: 452 loop : -1.35 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 76 TYR 0.019 0.001 TYR C 26 PHE 0.024 0.002 PHE A 342 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00269 (28232) covalent geometry : angle 0.59067 (38220) SS BOND : bond 0.00130 ( 4) SS BOND : angle 1.16472 ( 8) hydrogen bonds : bond 0.03510 ( 1272) hydrogen bonds : angle 4.87029 ( 3576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10015.50 seconds wall clock time: 171 minutes 49.22 seconds (10309.22 seconds total)