Starting phenix.real_space_refine on Sat Jul 4 21:21:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jd3_6632/07_2026/3jd3_6632.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd3_6632/07_2026/3jd3_6632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jd3_6632/07_2026/3jd3_6632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd3_6632/07_2026/3jd3_6632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jd3_6632/07_2026/3jd3_6632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd3_6632/07_2026/3jd3_6632.map" restraint_files = "/net/cci-nas-00/data/ceres_data/3jd3_6632/07_2026/3jd3_6632.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jd3_6632/07_2026/3jd3_6632.cif" } resolution = 3.6 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 114 5.16 5 C 15036 2.51 5 N 4188 2.21 5 O 4626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24006 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, D, E, F Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1B NAI A 603 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI A 603 " occ=0.35 residue: pdb=" C1B NAI B 603 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI B 603 " occ=0.35 residue: pdb=" C1B NAI C 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI C 601 " occ=0.35 residue: pdb=" C1B NAI D 603 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI D 603 " occ=0.35 residue: pdb=" C1B NAI E 603 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI E 603 " occ=0.35 residue: pdb=" C1B NAI F 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI F 601 " occ=0.35 Time building chain proxies: 7.71, per 1000 atoms: 0.32 Number of scatterers: 24006 At special positions: 0 Unit cell: (110.294, 116.67, 162.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 42 15.00 O 4626 8.00 N 4188 7.00 C 15036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 55 " distance=0.00 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 89 " distance=0.00 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 115 " distance=0.00 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 197 " distance=0.00 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 270 " distance=0.00 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 319 " distance=0.00 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: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 27 sheets defined 55.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.695A pdb=" N PHE A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 4.463A pdb=" N VAL A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.928A pdb=" N THR A 87 " --> pdb=" O GLN A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.806A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.627A pdb=" N MET A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.891A pdb=" N TYR A 190 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.529A pdb=" N HIS A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.828A pdb=" N ARG A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 removed outlier: 3.511A pdb=" N LEU A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.600A pdb=" N VAL A 339 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.683A pdb=" N ASP A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.893A pdb=" N LEU A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 374' Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.538A pdb=" N LEU A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 407 removed outlier: 3.577A pdb=" N GLU A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.963A pdb=" N ARG A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.866A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 497 removed outlier: 3.509A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY A 497 " --> pdb=" O TYR A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 32 removed outlier: 3.695A pdb=" N PHE B 16 " --> pdb=" O MET B 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 53 removed outlier: 4.463A pdb=" N VAL B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 removed outlier: 3.929A pdb=" N THR B 87 " --> pdb=" O GLN B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 87' Processing helix chain 'B' and resid 100 through 118 Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.806A pdb=" N ARG B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 154 " --> pdb=" O MET B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.627A pdb=" N MET B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.891A pdb=" N TYR B 190 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.529A pdb=" N HIS B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.828A pdb=" N ARG B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.512A pdb=" N LEU B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.600A pdb=" N VAL B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.683A pdb=" N ASP B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.892A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.540A pdb=" N LEU B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 407 removed outlier: 3.577A pdb=" N GLU B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.963A pdb=" N ARG B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.865A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 497 removed outlier: 3.508A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 497 " --> pdb=" O TYR B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 removed outlier: 3.695A pdb=" N PHE C 16 " --> pdb=" O MET C 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 17 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 53 removed outlier: 4.463A pdb=" N VAL C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 87 removed outlier: 3.928A pdb=" N THR C 87 " --> pdb=" O GLN C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 87' Processing helix chain 'C' and resid 100 through 118 Processing helix chain 'C' and resid 139 through 155 removed outlier: 3.807A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 154 " --> pdb=" O MET C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 removed outlier: 3.627A pdb=" N MET C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.891A pdb=" N TYR C 190 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.529A pdb=" N HIS C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.827A pdb=" N ARG C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 removed outlier: 3.511A pdb=" N LEU C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.600A pdb=" N VAL C 339 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.683A pdb=" N ASP C 357 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.893A pdb=" N LEU C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN C 374 " --> pdb=" O ASP C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 374' Processing helix chain 'C' and resid 375 through 388 removed outlier: 3.538A pdb=" N LEU C 386 " --> pdb=" O TYR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 407 removed outlier: 3.577A pdb=" N GLU C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.963A pdb=" N ARG C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.865A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 497 removed outlier: 3.509A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 497 " --> pdb=" O TYR C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 32 removed outlier: 3.695A pdb=" N PHE D 16 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE D 17 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 4.464A pdb=" N VAL D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 87 removed outlier: 3.928A pdb=" N THR D 87 " --> pdb=" O GLN D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 87' Processing helix chain 'D' and resid 100 through 118 Processing helix chain 'D' and resid 139 through 155 removed outlier: 3.806A pdb=" N ARG D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS D 154 " --> pdb=" O MET D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.627A pdb=" N MET D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.891A pdb=" N TYR D 190 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.529A pdb=" N HIS D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 241 through 244 Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.829A pdb=" N ARG D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 298 removed outlier: 3.511A pdb=" N LEU D 291 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.600A pdb=" N VAL D 339 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.683A pdb=" N ASP D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.893A pdb=" N LEU D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 374' Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.539A pdb=" N LEU D 386 " --> pdb=" O TYR D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 407 removed outlier: 3.576A pdb=" N GLU D 402 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 421 removed outlier: 3.964A pdb=" N ARG D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.865A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 497 removed outlier: 3.510A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY D 497 " --> pdb=" O TYR D 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 32 removed outlier: 3.696A pdb=" N PHE E 16 " --> pdb=" O MET E 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE E 17 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 53 removed outlier: 4.464A pdb=" N VAL E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 87 removed outlier: 3.929A pdb=" N THR E 87 " --> pdb=" O GLN E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 87' Processing helix chain 'E' and resid 100 through 118 Processing helix chain 'E' and resid 139 through 155 removed outlier: 3.806A pdb=" N ARG E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS E 154 " --> pdb=" O MET E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.627A pdb=" N MET E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.890A pdb=" N TYR E 190 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 224 removed outlier: 3.529A pdb=" N HIS E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.828A pdb=" N ARG E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 298 removed outlier: 3.511A pdb=" N LEU E 291 " --> pdb=" O ASP E 287 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.599A pdb=" N VAL E 339 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 363 removed outlier: 3.683A pdb=" N ASP E 357 " --> pdb=" O THR E 353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.893A pdb=" N LEU E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN E 374 " --> pdb=" O ASP E 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 369 through 374' Processing helix chain 'E' and resid 375 through 388 removed outlier: 3.540A pdb=" N LEU E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 407 removed outlier: 3.576A pdb=" N GLU E 402 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 421 removed outlier: 3.964A pdb=" N ARG E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS E 420 " --> pdb=" O SER E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 442 Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.865A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 497 removed outlier: 3.509A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY E 497 " --> pdb=" O TYR E 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 32 removed outlier: 3.696A pdb=" N PHE F 16 " --> pdb=" O MET F 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 53 removed outlier: 4.464A pdb=" N VAL F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG F 50 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 87 removed outlier: 3.929A pdb=" N THR F 87 " --> pdb=" O GLN F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 100 through 118 Processing helix chain 'F' and resid 139 through 155 removed outlier: 3.807A pdb=" N ARG F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS F 154 " --> pdb=" O MET F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 184 removed outlier: 3.627A pdb=" N MET F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.891A pdb=" N TYR F 190 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 224 removed outlier: 3.529A pdb=" N HIS F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 241 through 244 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.828A pdb=" N ARG F 261 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 298 removed outlier: 3.512A pdb=" N LEU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.600A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 363 removed outlier: 3.683A pdb=" N ASP F 357 " --> pdb=" O THR F 353 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 374 removed outlier: 3.893A pdb=" N LEU F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN F 374 " --> pdb=" O ASP F 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 369 through 374' Processing helix chain 'F' and resid 375 through 388 removed outlier: 3.538A pdb=" N LEU F 386 " --> pdb=" O TYR F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 407 removed outlier: 3.576A pdb=" N GLU F 402 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 421 removed outlier: 3.964A pdb=" N ARG F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS F 420 " --> pdb=" O SER F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 442 Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.865A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 497 removed outlier: 3.509A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY F 497 " --> pdb=" O TYR F 493 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 124 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 128 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 77 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 77 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY E 128 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY E 124 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=C, first strand: chain 'A' and resid 246 through 247 Processing sheet with id=D, first strand: chain 'A' and resid 272 through 275 removed outlier: 3.641A pdb=" N VAL A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.604A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=E Processing sheet with id=F, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY B 124 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 128 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 77 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 77 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 128 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY D 124 " --> pdb=" O HIS D 82 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=H, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=I, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.641A pdb=" N VAL B 273 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'B' and resid 343 through 345 removed outlier: 6.604A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=J Processing sheet with id=K, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.803A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY C 124 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY C 128 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 77 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 128 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY F 124 " --> pdb=" O HIS F 82 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=M, first strand: chain 'C' and resid 246 through 247 Processing sheet with id=N, first strand: chain 'C' and resid 272 through 275 removed outlier: 3.641A pdb=" N VAL C 273 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'C' and resid 343 through 345 removed outlier: 6.604A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=O Processing sheet with id=P, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=Q, first strand: chain 'D' and resid 246 through 247 Processing sheet with id=R, first strand: chain 'D' and resid 272 through 275 removed outlier: 3.640A pdb=" N VAL D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.604A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=S Processing sheet with id=T, first strand: chain 'E' and resid 65 through 66 Processing sheet with id=U, first strand: chain 'E' and resid 246 through 247 Processing sheet with id=V, first strand: chain 'E' and resid 272 through 275 removed outlier: 3.642A pdb=" N VAL E 273 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'E' and resid 343 through 345 removed outlier: 6.604A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=W Processing sheet with id=X, first strand: chain 'F' and resid 65 through 66 Processing sheet with id=Y, first strand: chain 'F' and resid 246 through 247 Processing sheet with id=Z, first strand: chain 'F' and resid 272 through 275 removed outlier: 3.641A pdb=" N VAL F 273 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'F' and resid 343 through 345 removed outlier: 6.604A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA 1044 hydrogen bonds defined for protein. 2934 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: 3.46 Time building geometry restraints manager: 3.10 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: 7771 1.34 - 1.45: 3883 1.45 - 1.57: 12646 1.57 - 1.69: 72 1.69 - 1.80: 192 Bond restraints: 24564 Sorted by residual: bond pdb=" C3N NAI E 602 " pdb=" C7N NAI E 602 " ideal model delta sigma weight residual 1.473 1.577 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3N NAI F 603 " pdb=" C7N NAI F 603 " ideal model delta sigma weight residual 1.473 1.577 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3N NAI C 603 " pdb=" C7N NAI C 603 " ideal model delta sigma weight residual 1.473 1.577 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3N NAI B 602 " pdb=" C7N NAI B 602 " ideal model delta sigma weight residual 1.473 1.576 -0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C3N NAI A 602 " pdb=" C7N NAI A 602 " ideal model delta sigma weight residual 1.473 1.576 -0.103 2.00e-02 2.50e+03 2.68e+01 ... (remaining 24559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 32710 3.14 - 6.28: 510 6.28 - 9.42: 68 9.42 - 12.56: 24 12.56 - 15.70: 6 Bond angle restraints: 33318 Sorted by residual: angle pdb=" O2A NAI E 602 " pdb=" PA NAI E 602 " pdb=" O5B NAI E 602 " ideal model delta sigma weight residual 105.34 121.04 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O2A NAI F 603 " pdb=" PA NAI F 603 " pdb=" O5B NAI F 603 " ideal model delta sigma weight residual 105.34 121.04 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O2A NAI C 603 " pdb=" PA NAI C 603 " pdb=" O5B NAI C 603 " ideal model delta sigma weight residual 105.34 121.03 -15.69 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O2A NAI A 602 " pdb=" PA NAI A 602 " pdb=" O5B NAI A 602 " ideal model delta sigma weight residual 105.34 121.03 -15.69 3.00e+00 1.11e-01 2.74e+01 angle pdb=" O2A NAI B 602 " pdb=" PA NAI B 602 " pdb=" O5B NAI B 602 " ideal model delta sigma weight residual 105.34 121.02 -15.68 3.00e+00 1.11e-01 2.73e+01 ... (remaining 33313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 14370 35.85 - 71.70: 66 71.70 - 107.54: 24 107.54 - 143.39: 6 143.39 - 179.24: 12 Dihedral angle restraints: 14478 sinusoidal: 6000 harmonic: 8478 Sorted by residual: dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 55 " pdb=" CB CYS B 55 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 89 " pdb=" SG CYS B 89 " pdb=" SG CYS B 89 " pdb=" CB CYS B 89 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 115 " pdb=" SG CYS B 115 " pdb=" SG CYS B 115 " pdb=" CB CYS B 115 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 ... (remaining 14475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3197 0.081 - 0.161: 367 0.161 - 0.242: 26 0.242 - 0.323: 16 0.323 - 0.403: 6 Chirality restraints: 3612 Sorted by residual: chirality pdb=" C3B NAI A 602 " pdb=" C2B NAI A 602 " pdb=" C4B NAI A 602 " pdb=" O3B NAI A 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.31 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C3B NAI E 602 " pdb=" C2B NAI E 602 " pdb=" C4B NAI E 602 " pdb=" O3B NAI E 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.31 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C3B NAI B 602 " pdb=" C2B NAI B 602 " pdb=" C4B NAI B 602 " pdb=" O3B NAI B 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.31 -0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 3609 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1B NAI B 602 " -0.030 2.00e-02 2.50e+03 1.32e-02 4.78e+00 pdb=" C2A NAI B 602 " 0.007 2.00e-02 2.50e+03 pdb=" C4A NAI B 602 " 0.012 2.00e-02 2.50e+03 pdb=" C5A NAI B 602 " 0.006 2.00e-02 2.50e+03 pdb=" C6A NAI B 602 " -0.003 2.00e-02 2.50e+03 pdb=" C8A NAI B 602 " 0.011 2.00e-02 2.50e+03 pdb=" N1A NAI B 602 " -0.004 2.00e-02 2.50e+03 pdb=" N3A NAI B 602 " 0.010 2.00e-02 2.50e+03 pdb=" N6A NAI B 602 " -0.021 2.00e-02 2.50e+03 pdb=" N7A NAI B 602 " 0.011 2.00e-02 2.50e+03 pdb=" N9A NAI B 602 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAI E 602 " -0.030 2.00e-02 2.50e+03 1.32e-02 4.77e+00 pdb=" C2A NAI E 602 " 0.007 2.00e-02 2.50e+03 pdb=" C4A NAI E 602 " 0.012 2.00e-02 2.50e+03 pdb=" C5A NAI E 602 " 0.006 2.00e-02 2.50e+03 pdb=" C6A NAI E 602 " -0.003 2.00e-02 2.50e+03 pdb=" C8A NAI E 602 " 0.010 2.00e-02 2.50e+03 pdb=" N1A NAI E 602 " -0.004 2.00e-02 2.50e+03 pdb=" N3A NAI E 602 " 0.010 2.00e-02 2.50e+03 pdb=" N6A NAI E 602 " -0.021 2.00e-02 2.50e+03 pdb=" N7A NAI E 602 " 0.011 2.00e-02 2.50e+03 pdb=" N9A NAI E 602 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAI A 602 " 0.030 2.00e-02 2.50e+03 1.31e-02 4.74e+00 pdb=" C2A NAI A 602 " -0.007 2.00e-02 2.50e+03 pdb=" C4A NAI A 602 " -0.012 2.00e-02 2.50e+03 pdb=" C5A NAI A 602 " -0.006 2.00e-02 2.50e+03 pdb=" C6A NAI A 602 " 0.003 2.00e-02 2.50e+03 pdb=" C8A NAI A 602 " -0.010 2.00e-02 2.50e+03 pdb=" N1A NAI A 602 " 0.004 2.00e-02 2.50e+03 pdb=" N3A NAI A 602 " -0.010 2.00e-02 2.50e+03 pdb=" N6A NAI A 602 " 0.021 2.00e-02 2.50e+03 pdb=" N7A NAI A 602 " -0.012 2.00e-02 2.50e+03 pdb=" N9A NAI A 602 " -0.001 2.00e-02 2.50e+03 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 826 2.68 - 3.23: 26763 3.23 - 3.79: 38069 3.79 - 4.34: 54437 4.34 - 4.90: 84494 Nonbonded interactions: 204589 Sorted by model distance: nonbonded pdb=" OG1 THR D 272 " pdb=" O ILE D 280 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR A 272 " pdb=" O ILE A 280 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR F 272 " pdb=" O ILE F 280 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR C 272 " pdb=" O ILE C 280 " model vdw 2.125 3.040 nonbonded pdb=" OG1 THR E 272 " pdb=" O ILE E 280 " model vdw 2.125 3.040 ... (remaining 204584 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 501 or resid 603)) selection = (chain 'B' and (resid 6 through 501 or resid 603)) selection = (chain 'C' and (resid 6 through 501 or resid 603)) selection = (chain 'D' and (resid 6 through 501 or resid 603)) selection = (chain 'E' and (resid 6 through 501 or resid 603)) selection = (chain 'F' and (resid 6 through 501 or resid 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.35 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.050 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.010 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.011 0.104 24564 Z= 0.512 Angle : 1.016 15.703 33324 Z= 0.488 Chirality : 0.058 0.403 3612 Planarity : 0.005 0.053 4230 Dihedral : 11.398 179.239 9066 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -5.32 (0.12), residues: 2964 helix: -3.56 (0.10), residues: 1368 sheet: -3.50 (0.22), residues: 354 loop : -3.31 (0.15), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 86 TYR 0.024 0.003 TYR F 262 PHE 0.019 0.003 PHE B 490 TRP 0.025 0.004 TRP A 281 HIS 0.009 0.002 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.01090 / 0.51 (24564) covalent geometry : angle 1.01652 / 0.49 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.29167 / 19.86 ( 1044) hydrogen bonds : angle 10.25956 / 7.24 ( 2934) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.8899 (mttt) cc_final: 0.8548 (mtpp) REVERT: A 403 ARG cc_start: 0.8595 (ttm170) cc_final: 0.8282 (ttm170) REVERT: A 500 PHE cc_start: 0.6645 (m-10) cc_final: 0.6184 (m-80) REVERT: B 143 LYS cc_start: 0.8870 (mttt) cc_final: 0.8534 (mtpp) REVERT: B 330 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7755 (mm-40) REVERT: B 403 ARG cc_start: 0.8590 (ttm170) cc_final: 0.8340 (ttm170) REVERT: B 500 PHE cc_start: 0.6518 (m-10) cc_final: 0.5783 (m-80) REVERT: C 143 LYS cc_start: 0.8841 (mttt) cc_final: 0.8528 (mtpp) REVERT: C 232 TYR cc_start: 0.7791 (m-10) cc_final: 0.6198 (m-10) REVERT: C 330 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7528 (mm-40) REVERT: C 500 PHE cc_start: 0.6742 (m-10) cc_final: 0.5607 (m-80) REVERT: D 143 LYS cc_start: 0.8897 (mttt) cc_final: 0.8549 (mtpp) REVERT: D 403 ARG cc_start: 0.8593 (ttm170) cc_final: 0.8258 (ttm170) REVERT: D 500 PHE cc_start: 0.6649 (m-10) cc_final: 0.6177 (m-80) REVERT: E 143 LYS cc_start: 0.8872 (mttt) cc_final: 0.8535 (mtpp) REVERT: E 330 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7756 (mm-40) REVERT: E 403 ARG cc_start: 0.8590 (ttm170) cc_final: 0.8328 (ttm170) REVERT: E 500 PHE cc_start: 0.6531 (m-10) cc_final: 0.5780 (m-80) REVERT: F 143 LYS cc_start: 0.8848 (mttt) cc_final: 0.8535 (mtpp) REVERT: F 232 TYR cc_start: 0.7791 (m-10) cc_final: 0.6190 (m-10) REVERT: F 330 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7531 (mm-40) REVERT: F 500 PHE cc_start: 0.6752 (m-10) cc_final: 0.5618 (m-80) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.1724 time to fit residues: 135.1231 Evaluate side-chains 270 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 40.0000 chunk 111 optimal weight: 8.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 81 GLN A 82 HIS A 85 HIS A 205 GLN A 463 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN B 56 ASN B 81 GLN B 82 HIS B 85 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN B 494 ASN C 56 ASN C 81 GLN C 82 HIS C 85 HIS C 205 GLN C 225 ASN C 414 GLN C 494 ASN D 56 ASN D 81 GLN D 82 HIS D 85 HIS D 205 GLN D 463 GLN D 484 ASN D 494 ASN E 56 ASN E 81 GLN E 82 HIS E 85 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN E 494 ASN F 56 ASN F 81 GLN F 82 HIS F 85 HIS F 205 GLN F 225 ASN F 414 GLN F 484 ASN F 494 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.102905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075776 restraints weight = 61123.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078643 restraints weight = 31493.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080455 restraints weight = 20874.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081534 restraints weight = 16386.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082173 restraints weight = 14302.269| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24564 Z= 0.165 Angle : 0.682 6.613 33324 Z= 0.352 Chirality : 0.045 0.167 3612 Planarity : 0.005 0.037 4230 Dihedral : 14.041 171.112 3474 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.08 % Allowed : 6.49 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -3.23 (0.14), residues: 2964 helix: -1.60 (0.11), residues: 1458 sheet: -3.22 (0.23), residues: 324 loop : -2.34 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 439 TYR 0.024 0.002 TYR C 407 PHE 0.024 0.002 PHE B 360 TRP 0.015 0.002 TRP E 178 HIS 0.004 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (24564) covalent geometry : angle 0.68228 / 0.35 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.05046 / 3.42 ( 1044) hydrogen bonds : angle 5.65009 / 4.04 ( 2934) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 391 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8561 (p0) cc_final: 0.8254 (p0) REVERT: A 143 LYS cc_start: 0.8775 (mttt) cc_final: 0.8392 (mtpp) REVERT: A 181 ASP cc_start: 0.7683 (t0) cc_final: 0.6896 (t0) REVERT: B 143 LYS cc_start: 0.8733 (mttt) cc_final: 0.8379 (mtpp) REVERT: B 181 ASP cc_start: 0.7555 (t0) cc_final: 0.7250 (t0) REVERT: B 233 MET cc_start: 0.7015 (tpt) cc_final: 0.6644 (tpt) REVERT: B 250 GLN cc_start: 0.7985 (tt0) cc_final: 0.6327 (tt0) REVERT: B 294 PHE cc_start: 0.8567 (m-10) cc_final: 0.8345 (m-10) REVERT: C 84 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7798 (mp10) REVERT: C 143 LYS cc_start: 0.8786 (mttt) cc_final: 0.8379 (mtpp) REVERT: C 181 ASP cc_start: 0.7633 (t0) cc_final: 0.7389 (t0) REVERT: C 250 GLN cc_start: 0.7913 (tt0) cc_final: 0.7029 (tt0) REVERT: C 294 PHE cc_start: 0.8587 (m-10) cc_final: 0.8319 (m-80) REVERT: D 143 LYS cc_start: 0.8772 (mttt) cc_final: 0.8361 (mtpp) REVERT: E 143 LYS cc_start: 0.8732 (mttt) cc_final: 0.8374 (mtpp) REVERT: E 181 ASP cc_start: 0.7569 (t0) cc_final: 0.7262 (t0) REVERT: E 233 MET cc_start: 0.7012 (tpt) cc_final: 0.6636 (tpt) REVERT: E 250 GLN cc_start: 0.7990 (tt0) cc_final: 0.6368 (tt0) REVERT: E 294 PHE cc_start: 0.8570 (m-10) cc_final: 0.8350 (m-10) REVERT: F 84 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7789 (mp10) REVERT: F 143 LYS cc_start: 0.8784 (mttt) cc_final: 0.8370 (mtpp) REVERT: F 181 ASP cc_start: 0.7635 (t0) cc_final: 0.7374 (t0) REVERT: F 250 GLN cc_start: 0.7922 (tt0) cc_final: 0.7021 (tt0) REVERT: F 294 PHE cc_start: 0.8585 (m-10) cc_final: 0.8320 (m-80) outliers start: 52 outliers final: 40 residues processed: 417 average time/residue: 0.1568 time to fit residues: 103.8283 Evaluate side-chains 300 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 85 HIS Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 28 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN A 494 ASN B 85 HIS B 205 GLN B 494 ASN C 484 ASN C 494 ASN D 85 HIS ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 ASN E 85 HIS E 205 GLN E 494 ASN F 484 ASN F 494 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.100241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073761 restraints weight = 61283.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.076571 restraints weight = 30610.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078344 restraints weight = 20046.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079421 restraints weight = 15653.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080058 restraints weight = 13607.098| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24564 Z= 0.141 Angle : 0.628 11.057 33324 Z= 0.317 Chirality : 0.044 0.177 3612 Planarity : 0.004 0.037 4230 Dihedral : 13.725 168.497 3474 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.80 % Allowed : 8.45 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -2.20 (0.14), residues: 2964 helix: -0.64 (0.12), residues: 1452 sheet: -2.94 (0.23), residues: 318 loop : -1.94 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 86 TYR 0.021 0.001 TYR B 407 PHE 0.018 0.002 PHE F 490 TRP 0.013 0.001 TRP A 72 HIS 0.007 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (24564) covalent geometry : angle 0.62839 / 0.32 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.04199 / 2.82 ( 1044) hydrogen bonds : angle 4.99352 / 3.58 ( 2934) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 306 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8585 (p0) cc_final: 0.8199 (p0) REVERT: A 143 LYS cc_start: 0.8794 (mttt) cc_final: 0.8462 (mtpp) REVERT: A 366 MET cc_start: 0.7424 (ttm) cc_final: 0.7216 (ttm) REVERT: B 25 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8247 (mm-30) REVERT: B 143 LYS cc_start: 0.8750 (mttt) cc_final: 0.8369 (mtpp) REVERT: B 169 MET cc_start: 0.7949 (mmm) cc_final: 0.7696 (mmp) REVERT: B 181 ASP cc_start: 0.7614 (t0) cc_final: 0.7373 (t0) REVERT: B 232 TYR cc_start: 0.7371 (m-10) cc_final: 0.4826 (m-80) REVERT: B 330 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7523 (mm-40) REVERT: C 84 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7959 (mp10) REVERT: C 143 LYS cc_start: 0.8796 (mttt) cc_final: 0.8379 (mtpp) REVERT: C 181 ASP cc_start: 0.7802 (t0) cc_final: 0.7270 (t0) REVERT: C 233 MET cc_start: 0.7031 (mmp) cc_final: 0.6787 (tpt) REVERT: C 294 PHE cc_start: 0.8606 (m-10) cc_final: 0.8340 (m-80) REVERT: C 330 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7464 (mm-40) REVERT: D 143 LYS cc_start: 0.8795 (mttt) cc_final: 0.8385 (mtpp) REVERT: E 25 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8247 (mm-30) REVERT: E 143 LYS cc_start: 0.8748 (mttt) cc_final: 0.8372 (mtpp) REVERT: E 181 ASP cc_start: 0.7636 (t0) cc_final: 0.7394 (t0) REVERT: E 233 MET cc_start: 0.7064 (tpt) cc_final: 0.6819 (tpt) REVERT: E 294 PHE cc_start: 0.8551 (m-10) cc_final: 0.8345 (m-10) REVERT: E 330 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7514 (mm-40) REVERT: F 84 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7941 (mp10) REVERT: F 143 LYS cc_start: 0.8800 (mttt) cc_final: 0.8365 (mtpp) REVERT: F 181 ASP cc_start: 0.7819 (t0) cc_final: 0.7287 (t0) REVERT: F 233 MET cc_start: 0.7015 (mmp) cc_final: 0.6782 (tpt) REVERT: F 294 PHE cc_start: 0.8600 (m-10) cc_final: 0.8364 (m-80) REVERT: F 330 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7467 (mm-40) outliers start: 70 outliers final: 34 residues processed: 353 average time/residue: 0.1518 time to fit residues: 85.0213 Evaluate side-chains 271 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 232 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 140 optimal weight: 0.0370 chunk 265 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 214 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 484 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 HIS F 484 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.099952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073432 restraints weight = 60947.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.076216 restraints weight = 30418.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078026 restraints weight = 19890.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079082 restraints weight = 15469.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079750 restraints weight = 13447.569| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24564 Z= 0.139 Angle : 0.600 9.970 33324 Z= 0.301 Chirality : 0.043 0.169 3612 Planarity : 0.004 0.038 4230 Dihedral : 13.516 166.665 3474 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.24 % Allowed : 10.06 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -1.61 (0.15), residues: 2964 helix: -0.10 (0.13), residues: 1458 sheet: -2.65 (0.24), residues: 318 loop : -1.73 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 403 TYR 0.020 0.001 TYR A 407 PHE 0.019 0.002 PHE F 500 TRP 0.013 0.001 TRP A 72 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (24564) covalent geometry : angle 0.60006 / 0.30 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03780 / 2.54 ( 1044) hydrogen bonds : angle 4.67455 / 3.35 ( 2934) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 287 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8602 (p0) cc_final: 0.8181 (p0) REVERT: A 143 LYS cc_start: 0.8806 (mttt) cc_final: 0.8420 (mtpp) REVERT: A 232 TYR cc_start: 0.7786 (m-80) cc_final: 0.7540 (m-10) REVERT: A 294 PHE cc_start: 0.8531 (m-10) cc_final: 0.8207 (m-80) REVERT: B 25 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: B 143 LYS cc_start: 0.8772 (mttt) cc_final: 0.8512 (mtpp) REVERT: B 169 MET cc_start: 0.8015 (mmm) cc_final: 0.7758 (mmp) REVERT: B 181 ASP cc_start: 0.7814 (t70) cc_final: 0.7409 (t0) REVERT: B 330 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7676 (mm-40) REVERT: B 437 GLN cc_start: 0.8320 (tp40) cc_final: 0.8061 (tp-100) REVERT: C 84 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7871 (mp10) REVERT: C 143 LYS cc_start: 0.8792 (mttt) cc_final: 0.8391 (mtpp) REVERT: C 181 ASP cc_start: 0.7833 (t0) cc_final: 0.7250 (t0) REVERT: C 233 MET cc_start: 0.7005 (mmp) cc_final: 0.6799 (tpt) REVERT: C 250 GLN cc_start: 0.7956 (tt0) cc_final: 0.7476 (pt0) REVERT: C 437 GLN cc_start: 0.8442 (tp40) cc_final: 0.8167 (tp-100) REVERT: D 102 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8069 (p0) REVERT: D 143 LYS cc_start: 0.8810 (mttt) cc_final: 0.8429 (mtpp) REVERT: D 294 PHE cc_start: 0.8523 (m-10) cc_final: 0.8206 (m-80) REVERT: E 25 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8249 (mm-30) REVERT: E 143 LYS cc_start: 0.8772 (mttt) cc_final: 0.8511 (mtpp) REVERT: E 181 ASP cc_start: 0.7838 (t70) cc_final: 0.7432 (t0) REVERT: E 233 MET cc_start: 0.7118 (tpt) cc_final: 0.6912 (tpt) REVERT: E 330 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7637 (mm-40) REVERT: F 84 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7855 (mp10) REVERT: F 143 LYS cc_start: 0.8801 (mttt) cc_final: 0.8382 (mtpp) REVERT: F 181 ASP cc_start: 0.7841 (t0) cc_final: 0.7259 (t0) REVERT: F 233 MET cc_start: 0.7013 (mmp) cc_final: 0.6806 (tpt) REVERT: F 250 GLN cc_start: 0.7954 (tt0) cc_final: 0.7473 (pt0) REVERT: F 437 GLN cc_start: 0.8419 (tp40) cc_final: 0.8165 (tp-100) outliers start: 56 outliers final: 39 residues processed: 331 average time/residue: 0.1583 time to fit residues: 84.2434 Evaluate side-chains 278 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 31 optimal weight: 6.9990 chunk 125 optimal weight: 0.0050 chunk 149 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 276 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 287 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 330 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN E 330 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073496 restraints weight = 60561.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.076289 restraints weight = 30369.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078082 restraints weight = 19864.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079167 restraints weight = 15435.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.079826 restraints weight = 13370.017| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24564 Z= 0.130 Angle : 0.578 9.292 33324 Z= 0.289 Chirality : 0.043 0.147 3612 Planarity : 0.004 0.037 4230 Dihedral : 13.348 164.055 3474 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.56 % Allowed : 10.34 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -1.22 (0.15), residues: 2964 helix: 0.12 (0.13), residues: 1470 sheet: -2.05 (0.25), residues: 378 loop : -1.47 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 363 TYR 0.019 0.001 TYR A 407 PHE 0.023 0.002 PHE A 500 TRP 0.011 0.001 TRP A 72 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (24564) covalent geometry : angle 0.57788 / 0.29 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03578 / 2.41 ( 1044) hydrogen bonds : angle 4.45127 / 3.19 ( 2934) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 264 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8609 (p0) cc_final: 0.8168 (p0) REVERT: A 143 LYS cc_start: 0.8838 (mttt) cc_final: 0.8454 (mtpp) REVERT: A 263 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8544 (mt) REVERT: A 294 PHE cc_start: 0.8603 (m-10) cc_final: 0.8253 (m-80) REVERT: B 25 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: B 143 LYS cc_start: 0.8802 (mttt) cc_final: 0.8570 (mtpp) REVERT: B 181 ASP cc_start: 0.7862 (t70) cc_final: 0.7422 (t0) REVERT: B 250 GLN cc_start: 0.8023 (tt0) cc_final: 0.6462 (pt0) REVERT: B 435 GLU cc_start: 0.8327 (mp0) cc_final: 0.7942 (mp0) REVERT: B 437 GLN cc_start: 0.8357 (tp40) cc_final: 0.8109 (tp-100) REVERT: C 143 LYS cc_start: 0.8793 (mttt) cc_final: 0.8401 (mtpp) REVERT: C 181 ASP cc_start: 0.7853 (t0) cc_final: 0.7240 (t0) REVERT: C 233 MET cc_start: 0.7019 (mmp) cc_final: 0.6761 (tpt) REVERT: C 250 GLN cc_start: 0.7822 (tt0) cc_final: 0.7471 (pt0) REVERT: C 437 GLN cc_start: 0.8444 (tp40) cc_final: 0.8174 (tp-100) REVERT: D 102 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8045 (p0) REVERT: D 143 LYS cc_start: 0.8844 (mttt) cc_final: 0.8465 (mtpp) REVERT: D 263 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8512 (mt) REVERT: D 294 PHE cc_start: 0.8594 (m-10) cc_final: 0.8253 (m-80) REVERT: E 25 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8233 (mm-30) REVERT: E 143 LYS cc_start: 0.8795 (mttt) cc_final: 0.8537 (mtpp) REVERT: E 181 ASP cc_start: 0.7880 (t70) cc_final: 0.7423 (t0) REVERT: E 233 MET cc_start: 0.7057 (tpt) cc_final: 0.6845 (tpt) REVERT: E 294 PHE cc_start: 0.8557 (m-10) cc_final: 0.8244 (m-10) REVERT: E 330 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7673 (mm-40) REVERT: E 437 GLN cc_start: 0.8278 (tp40) cc_final: 0.8027 (tp-100) REVERT: F 143 LYS cc_start: 0.8796 (mttt) cc_final: 0.8387 (mtpp) REVERT: F 181 ASP cc_start: 0.7871 (t0) cc_final: 0.7271 (t0) REVERT: F 233 MET cc_start: 0.7026 (mmp) cc_final: 0.6781 (tpt) REVERT: F 250 GLN cc_start: 0.7810 (tt0) cc_final: 0.7456 (pt0) REVERT: F 294 PHE cc_start: 0.8582 (m-10) cc_final: 0.8279 (m-80) REVERT: F 437 GLN cc_start: 0.8422 (tp40) cc_final: 0.8177 (tp-100) outliers start: 64 outliers final: 42 residues processed: 312 average time/residue: 0.1617 time to fit residues: 82.5417 Evaluate side-chains 286 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 267 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 271 optimal weight: 40.0000 chunk 210 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN E 330 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.099062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072294 restraints weight = 60809.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.075044 restraints weight = 30561.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076802 restraints weight = 20050.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.077892 restraints weight = 15643.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078536 restraints weight = 13576.511| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24564 Z= 0.169 Angle : 0.598 8.039 33324 Z= 0.302 Chirality : 0.044 0.148 3612 Planarity : 0.004 0.035 4230 Dihedral : 13.206 161.517 3474 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.84 % Allowed : 11.54 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -1.20 (0.15), residues: 2964 helix: 0.11 (0.13), residues: 1506 sheet: -2.07 (0.24), residues: 390 loop : -1.45 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 462 TYR 0.020 0.001 TYR C 407 PHE 0.023 0.002 PHE D 500 TRP 0.010 0.001 TRP A 72 HIS 0.004 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (24564) covalent geometry : angle 0.59756 / 0.30 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03806 / 2.59 ( 1044) hydrogen bonds : angle 4.49906 / 3.23 ( 2934) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 252 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8630 (p0) cc_final: 0.8221 (p0) REVERT: A 119 ASP cc_start: 0.8069 (t0) cc_final: 0.7659 (t0) REVERT: A 143 LYS cc_start: 0.8844 (mttt) cc_final: 0.8465 (mtpp) REVERT: A 250 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: A 294 PHE cc_start: 0.8655 (m-10) cc_final: 0.8334 (m-80) REVERT: B 25 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8228 (mm-30) REVERT: B 143 LYS cc_start: 0.8847 (mttt) cc_final: 0.8594 (mtpp) REVERT: B 169 MET cc_start: 0.8216 (mmp) cc_final: 0.7982 (mmp) REVERT: B 181 ASP cc_start: 0.7851 (t70) cc_final: 0.7375 (t0) REVERT: B 233 MET cc_start: 0.7481 (tpt) cc_final: 0.7220 (tpt) REVERT: B 435 GLU cc_start: 0.8365 (mp0) cc_final: 0.8035 (mp0) REVERT: B 437 GLN cc_start: 0.8375 (tp40) cc_final: 0.8150 (tp-100) REVERT: C 143 LYS cc_start: 0.8788 (mttt) cc_final: 0.8434 (mtpp) REVERT: C 181 ASP cc_start: 0.7848 (t0) cc_final: 0.7371 (t70) REVERT: C 233 MET cc_start: 0.6998 (mmp) cc_final: 0.6778 (tpt) REVERT: C 250 GLN cc_start: 0.7850 (tt0) cc_final: 0.7427 (pt0) REVERT: C 294 PHE cc_start: 0.8648 (m-10) cc_final: 0.8363 (m-80) REVERT: C 437 GLN cc_start: 0.8471 (tp40) cc_final: 0.8212 (tp-100) REVERT: C 465 MET cc_start: 0.8220 (mmm) cc_final: 0.7950 (mmm) REVERT: D 102 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8096 (p0) REVERT: D 143 LYS cc_start: 0.8851 (mttt) cc_final: 0.8474 (mtpp) REVERT: D 250 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7435 (pt0) REVERT: D 294 PHE cc_start: 0.8648 (m-10) cc_final: 0.8333 (m-80) REVERT: E 25 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8232 (mm-30) REVERT: E 143 LYS cc_start: 0.8798 (mttt) cc_final: 0.8582 (mtpp) REVERT: E 181 ASP cc_start: 0.7888 (t70) cc_final: 0.7410 (t0) REVERT: E 233 MET cc_start: 0.6994 (tpt) cc_final: 0.6788 (tpt) REVERT: E 294 PHE cc_start: 0.8668 (m-10) cc_final: 0.8346 (m-80) REVERT: E 437 GLN cc_start: 0.8356 (tp40) cc_final: 0.8109 (tp-100) REVERT: F 143 LYS cc_start: 0.8811 (mttt) cc_final: 0.8428 (mtpp) REVERT: F 181 ASP cc_start: 0.7835 (t0) cc_final: 0.7195 (t0) REVERT: F 233 MET cc_start: 0.7020 (mmp) cc_final: 0.6778 (tpt) REVERT: F 250 GLN cc_start: 0.7830 (tt0) cc_final: 0.7420 (pt0) REVERT: F 294 PHE cc_start: 0.8644 (m-10) cc_final: 0.8360 (m-80) REVERT: F 437 GLN cc_start: 0.8448 (tp40) cc_final: 0.8226 (tp-100) REVERT: F 465 MET cc_start: 0.8168 (mmm) cc_final: 0.7870 (mmm) outliers start: 71 outliers final: 56 residues processed: 302 average time/residue: 0.1501 time to fit residues: 76.0550 Evaluate side-chains 299 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 238 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLN Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 131 optimal weight: 9.9990 chunk 272 optimal weight: 0.0020 chunk 110 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 270 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072425 restraints weight = 60780.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.075172 restraints weight = 30648.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076946 restraints weight = 20159.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078005 restraints weight = 15756.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078625 restraints weight = 13728.418| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24564 Z= 0.155 Angle : 0.595 7.799 33324 Z= 0.299 Chirality : 0.043 0.142 3612 Planarity : 0.004 0.039 4230 Dihedral : 12.757 154.380 3474 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.17 % Allowed : 12.34 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -1.00 (0.15), residues: 2964 helix: 0.30 (0.13), residues: 1470 sheet: -1.90 (0.25), residues: 390 loop : -1.36 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 462 TYR 0.019 0.001 TYR C 407 PHE 0.018 0.002 PHE D 500 TRP 0.009 0.001 TRP A 72 HIS 0.004 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (24564) covalent geometry : angle 0.59502 / 0.30 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03662 / 2.48 ( 1044) hydrogen bonds : angle 4.43548 / 3.19 ( 2934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8619 (p0) cc_final: 0.8194 (p0) REVERT: A 119 ASP cc_start: 0.8038 (t0) cc_final: 0.7628 (t0) REVERT: A 143 LYS cc_start: 0.8842 (mttt) cc_final: 0.8451 (mtpp) REVERT: A 233 MET cc_start: 0.7349 (mmt) cc_final: 0.7121 (mmm) REVERT: A 250 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: A 294 PHE cc_start: 0.8732 (m-10) cc_final: 0.8412 (m-80) REVERT: A 330 GLN cc_start: 0.8464 (tp40) cc_final: 0.8261 (tp40) REVERT: B 25 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: B 143 LYS cc_start: 0.8852 (mttt) cc_final: 0.8607 (mtpp) REVERT: B 169 MET cc_start: 0.8248 (mmp) cc_final: 0.7996 (mmp) REVERT: B 181 ASP cc_start: 0.7828 (t70) cc_final: 0.7344 (t0) REVERT: B 233 MET cc_start: 0.7510 (tpt) cc_final: 0.7248 (tpt) REVERT: B 435 GLU cc_start: 0.8353 (mp0) cc_final: 0.8067 (mp0) REVERT: B 437 GLN cc_start: 0.8351 (tp40) cc_final: 0.8051 (tp-100) REVERT: C 143 LYS cc_start: 0.8789 (mttt) cc_final: 0.8449 (mtpp) REVERT: C 181 ASP cc_start: 0.7837 (t0) cc_final: 0.7339 (t0) REVERT: C 250 GLN cc_start: 0.7844 (tt0) cc_final: 0.7462 (pt0) REVERT: C 294 PHE cc_start: 0.8751 (m-10) cc_final: 0.8472 (m-10) REVERT: C 437 GLN cc_start: 0.8437 (tp40) cc_final: 0.8190 (tp-100) REVERT: D 102 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8092 (p0) REVERT: D 143 LYS cc_start: 0.8850 (mttt) cc_final: 0.8475 (mtpp) REVERT: D 294 PHE cc_start: 0.8729 (m-10) cc_final: 0.8415 (m-80) REVERT: E 25 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: E 143 LYS cc_start: 0.8841 (mttt) cc_final: 0.8603 (mtpp) REVERT: E 169 MET cc_start: 0.8208 (mmp) cc_final: 0.7952 (mmp) REVERT: E 181 ASP cc_start: 0.7845 (t70) cc_final: 0.7358 (t0) REVERT: E 294 PHE cc_start: 0.8741 (m-10) cc_final: 0.8465 (m-80) REVERT: E 437 GLN cc_start: 0.8360 (tp40) cc_final: 0.8121 (tp-100) REVERT: F 143 LYS cc_start: 0.8811 (mttt) cc_final: 0.8440 (mtpp) REVERT: F 181 ASP cc_start: 0.7831 (t0) cc_final: 0.7189 (t0) REVERT: F 233 MET cc_start: 0.7014 (mmp) cc_final: 0.6803 (tpt) REVERT: F 250 GLN cc_start: 0.7846 (tt0) cc_final: 0.7463 (pt0) REVERT: F 294 PHE cc_start: 0.8751 (m-10) cc_final: 0.8477 (m-10) REVERT: F 437 GLN cc_start: 0.8429 (tp40) cc_final: 0.8120 (tp-100) outliers start: 79 outliers final: 60 residues processed: 315 average time/residue: 0.1526 time to fit residues: 79.7590 Evaluate side-chains 301 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 237 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 2 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.099365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.072812 restraints weight = 60264.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075597 restraints weight = 30236.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077360 restraints weight = 19782.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078445 restraints weight = 15435.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079093 restraints weight = 13415.882| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24564 Z= 0.147 Angle : 0.593 9.719 33324 Z= 0.297 Chirality : 0.043 0.142 3612 Planarity : 0.004 0.034 4230 Dihedral : 11.877 177.381 3474 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.80 % Allowed : 12.86 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -0.89 (0.15), residues: 2964 helix: 0.30 (0.13), residues: 1494 sheet: -1.84 (0.24), residues: 390 loop : -1.21 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 462 TYR 0.016 0.001 TYR F 407 PHE 0.016 0.002 PHE D 500 TRP 0.010 0.001 TRP A 72 HIS 0.004 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (24564) covalent geometry : angle 0.59298 / 0.30 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03580 / 2.42 ( 1044) hydrogen bonds : angle 4.37613 / 3.14 ( 2934) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 253 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8615 (p0) cc_final: 0.8183 (p0) REVERT: A 119 ASP cc_start: 0.8036 (t0) cc_final: 0.7631 (t0) REVERT: A 143 LYS cc_start: 0.8834 (mttt) cc_final: 0.8435 (mtpp) REVERT: A 233 MET cc_start: 0.7316 (mmt) cc_final: 0.6986 (mmm) REVERT: A 294 PHE cc_start: 0.8789 (m-10) cc_final: 0.8447 (m-80) REVERT: A 330 GLN cc_start: 0.8443 (tp40) cc_final: 0.8056 (tp40) REVERT: B 25 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: B 143 LYS cc_start: 0.8849 (mttt) cc_final: 0.8480 (mtpp) REVERT: B 181 ASP cc_start: 0.7828 (t70) cc_final: 0.7327 (t0) REVERT: B 233 MET cc_start: 0.7497 (tpt) cc_final: 0.7244 (tpt) REVERT: B 435 GLU cc_start: 0.8331 (mp0) cc_final: 0.8074 (mp0) REVERT: B 437 GLN cc_start: 0.8364 (tp40) cc_final: 0.8078 (tp-100) REVERT: C 143 LYS cc_start: 0.8788 (mttt) cc_final: 0.8448 (mtpp) REVERT: C 181 ASP cc_start: 0.7847 (t0) cc_final: 0.7360 (t70) REVERT: C 250 GLN cc_start: 0.7879 (tt0) cc_final: 0.6998 (pt0) REVERT: C 260 MET cc_start: 0.8522 (tmm) cc_final: 0.7670 (ptm) REVERT: C 330 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7635 (mt0) REVERT: C 437 GLN cc_start: 0.8446 (tp40) cc_final: 0.8223 (tp-100) REVERT: C 465 MET cc_start: 0.8115 (mmm) cc_final: 0.7680 (mmm) REVERT: D 102 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8073 (p0) REVERT: D 143 LYS cc_start: 0.8843 (mttt) cc_final: 0.8446 (mtpp) REVERT: D 294 PHE cc_start: 0.8793 (m-10) cc_final: 0.8449 (m-80) REVERT: E 25 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8231 (mm-30) REVERT: E 143 LYS cc_start: 0.8851 (mttt) cc_final: 0.8491 (mtpp) REVERT: E 169 MET cc_start: 0.8247 (mmp) cc_final: 0.8034 (mmp) REVERT: E 181 ASP cc_start: 0.7847 (t70) cc_final: 0.7357 (t0) REVERT: E 260 MET cc_start: 0.8434 (tmm) cc_final: 0.7875 (ptp) REVERT: E 294 PHE cc_start: 0.8747 (m-10) cc_final: 0.8472 (m-80) REVERT: E 437 GLN cc_start: 0.8366 (tp40) cc_final: 0.8143 (tp-100) REVERT: E 465 MET cc_start: 0.7281 (mtm) cc_final: 0.7066 (mtm) REVERT: F 143 LYS cc_start: 0.8800 (mttt) cc_final: 0.8436 (mtpp) REVERT: F 181 ASP cc_start: 0.7843 (t0) cc_final: 0.7358 (t70) REVERT: F 250 GLN cc_start: 0.7869 (tt0) cc_final: 0.7503 (pt0) REVERT: F 260 MET cc_start: 0.8523 (tmm) cc_final: 0.7666 (ptm) REVERT: F 294 PHE cc_start: 0.8739 (m-10) cc_final: 0.8514 (m-10) REVERT: F 437 GLN cc_start: 0.8431 (tp40) cc_final: 0.8153 (tp-100) REVERT: F 465 MET cc_start: 0.8161 (mmm) cc_final: 0.7599 (mmm) outliers start: 70 outliers final: 58 residues processed: 305 average time/residue: 0.1464 time to fit residues: 73.5408 Evaluate side-chains 307 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 50 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 172 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 330 GLN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.098271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071589 restraints weight = 60703.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074287 restraints weight = 30630.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.076050 restraints weight = 20204.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077059 restraints weight = 15806.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077720 restraints weight = 13817.846| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24564 Z= 0.195 Angle : 0.634 10.494 33324 Z= 0.318 Chirality : 0.044 0.239 3612 Planarity : 0.004 0.034 4230 Dihedral : 11.393 174.122 3474 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.08 % Allowed : 12.82 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -0.99 (0.15), residues: 2964 helix: 0.20 (0.13), residues: 1494 sheet: -1.86 (0.24), residues: 390 loop : -1.25 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 462 TYR 0.020 0.002 TYR F 232 PHE 0.019 0.002 PHE C 294 TRP 0.009 0.001 TRP A 72 HIS 0.004 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (24564) covalent geometry : angle 0.63444 / 0.32 (33318) SS BOND : angle 0.00000 / 0.00 ( 6) hydrogen bonds : bond 0.03891 / 2.65 ( 1044) hydrogen bonds : angle 4.52980 / 3.25 ( 2934) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 247 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8651 (p0) cc_final: 0.8248 (p0) REVERT: A 143 LYS cc_start: 0.8831 (mttt) cc_final: 0.8429 (mtpp) REVERT: A 233 MET cc_start: 0.7407 (mmt) cc_final: 0.7029 (mmm) REVERT: A 294 PHE cc_start: 0.8812 (m-10) cc_final: 0.8471 (m-80) REVERT: A 330 GLN cc_start: 0.8440 (tp40) cc_final: 0.8060 (tp40) REVERT: B 25 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: B 143 LYS cc_start: 0.8845 (mttt) cc_final: 0.8601 (mtpp) REVERT: B 181 ASP cc_start: 0.7803 (t70) cc_final: 0.7295 (t0) REVERT: B 233 MET cc_start: 0.7499 (tpt) cc_final: 0.7255 (tpt) REVERT: B 437 GLN cc_start: 0.8392 (tp40) cc_final: 0.8114 (tp-100) REVERT: C 143 LYS cc_start: 0.8801 (mttt) cc_final: 0.8457 (mtpp) REVERT: C 181 ASP cc_start: 0.7835 (t0) cc_final: 0.7345 (t70) REVERT: C 250 GLN cc_start: 0.7903 (tt0) cc_final: 0.7111 (tm-30) REVERT: C 330 GLN cc_start: 0.7908 (mm110) cc_final: 0.7541 (tt0) REVERT: C 437 GLN cc_start: 0.8456 (tp40) cc_final: 0.8237 (tp-100) REVERT: C 465 MET cc_start: 0.8186 (mmm) cc_final: 0.7873 (mmm) REVERT: D 102 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8138 (p0) REVERT: D 143 LYS cc_start: 0.8837 (mttt) cc_final: 0.8453 (mtpp) REVERT: D 250 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: D 294 PHE cc_start: 0.8800 (m-10) cc_final: 0.8468 (m-80) REVERT: D 366 MET cc_start: 0.7596 (ttt) cc_final: 0.7370 (ttm) REVERT: E 25 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: E 143 LYS cc_start: 0.8855 (mttt) cc_final: 0.8612 (mtpp) REVERT: E 169 MET cc_start: 0.8286 (mmp) cc_final: 0.8076 (mmp) REVERT: E 181 ASP cc_start: 0.7802 (t70) cc_final: 0.7301 (t0) REVERT: E 233 MET cc_start: 0.7500 (mmt) cc_final: 0.7259 (mmm) REVERT: E 294 PHE cc_start: 0.8765 (m-10) cc_final: 0.8486 (m-80) REVERT: E 437 GLN cc_start: 0.8377 (tp40) cc_final: 0.8169 (tp-100) REVERT: F 143 LYS cc_start: 0.8812 (mttt) cc_final: 0.8446 (mtpp) REVERT: F 181 ASP cc_start: 0.7847 (t0) cc_final: 0.7371 (t70) REVERT: F 233 MET cc_start: 0.7562 (mmm) cc_final: 0.7069 (mmm) REVERT: F 250 GLN cc_start: 0.7925 (tt0) cc_final: 0.7509 (pt0) REVERT: F 260 MET cc_start: 0.8522 (tmm) cc_final: 0.7721 (ptm) REVERT: F 437 GLN cc_start: 0.8434 (tp40) cc_final: 0.8169 (tp-100) REVERT: F 465 MET cc_start: 0.7993 (mmm) cc_final: 0.7658 (mmm) outliers start: 77 outliers final: 64 residues processed: 299 average time/residue: 0.1422 time to fit residues: 70.4492 Evaluate side-chains 309 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 241 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 250 GLN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4196 > 50: distance: 62 - 95: 35.042 distance: 68 - 103: 32.356 distance: 73 - 74: 11.483 distance: 74 - 75: 15.925 distance: 74 - 77: 10.599 distance: 75 - 76: 21.914 distance: 75 - 87: 5.455 distance: 77 - 78: 16.791 distance: 78 - 79: 6.610 distance: 78 - 80: 8.564 distance: 79 - 81: 10.684 distance: 80 - 82: 10.216 distance: 80 - 83: 12.078 distance: 81 - 82: 5.615 distance: 82 - 84: 9.557 distance: 83 - 85: 10.843 distance: 84 - 86: 6.320 distance: 85 - 86: 10.770 distance: 87 - 88: 15.272 distance: 88 - 89: 9.803 distance: 88 - 91: 7.950 distance: 89 - 90: 7.041 distance: 89 - 95: 3.200 distance: 91 - 92: 20.542 distance: 92 - 93: 20.419 distance: 92 - 94: 32.667 distance: 95 - 96: 21.814 distance: 96 - 97: 20.089 distance: 96 - 99: 4.902 distance: 97 - 98: 16.937 distance: 97 - 103: 51.172 distance: 99 - 100: 32.730 distance: 100 - 101: 9.635 distance: 100 - 102: 8.212 distance: 103 - 104: 22.245 distance: 104 - 105: 15.573 distance: 104 - 107: 15.709 distance: 105 - 106: 3.564 distance: 105 - 111: 3.255 distance: 107 - 108: 25.714 distance: 108 - 109: 8.465 distance: 108 - 110: 41.057 distance: 112 - 113: 7.564 distance: 112 - 115: 16.103 distance: 113 - 114: 17.302 distance: 113 - 119: 3.643 distance: 115 - 116: 23.147 distance: 116 - 117: 23.257 distance: 116 - 118: 38.105 distance: 119 - 120: 23.026 distance: 120 - 121: 21.450 distance: 120 - 123: 29.668 distance: 121 - 122: 30.830 distance: 121 - 127: 24.311 distance: 123 - 124: 25.924 distance: 124 - 125: 18.960 distance: 127 - 128: 35.263 distance: 128 - 129: 6.603 distance: 128 - 131: 18.117 distance: 129 - 137: 18.364 distance: 131 - 132: 10.246 distance: 132 - 133: 27.417 distance: 132 - 134: 25.675 distance: 133 - 135: 10.244 distance: 134 - 136: 23.980 distance: 135 - 136: 29.545 distance: 137 - 138: 4.544 distance: 138 - 139: 15.188 distance: 138 - 141: 33.089 distance: 139 - 140: 16.937 distance: 139 - 144: 6.172 distance: 141 - 142: 20.627 distance: 144 - 145: 6.373 distance: 145 - 146: 35.493 distance: 145 - 148: 4.980 distance: 146 - 147: 34.278 distance: 146 - 150: 8.446 distance: 148 - 149: 34.900 distance: 150 - 151: 3.333 distance: 151 - 152: 8.609 distance: 151 - 154: 10.338 distance: 152 - 153: 8.621 distance: 152 - 162: 29.013 distance: 154 - 155: 7.101 distance: 155 - 156: 7.939 distance: 155 - 157: 40.962 distance: 156 - 158: 24.367 distance: 157 - 159: 3.330 distance: 158 - 160: 33.013 distance: 159 - 160: 24.110 distance: 160 - 161: 5.596