Starting phenix.real_space_refine on Fri Sep 19 05:49:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd3_6632/09_2025/3jd3_6632.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd3_6632/09_2025/3jd3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3jd3_6632/09_2025/3jd3_6632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd3_6632/09_2025/3jd3_6632.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd3_6632/09_2025/3jd3_6632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd3_6632/09_2025/3jd3_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 5.88, per 1000 atoms: 0.24 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: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.7 microseconds 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: 1.18 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: 4.91 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 14796 35.85 - 71.70: 252 71.70 - 107.54: 12 107.54 - 143.39: 6 143.39 - 179.24: 12 Dihedral angle restraints: 15078 sinusoidal: 6600 harmonic: 8478 Sorted by residual: dihedral pdb=" C5' GTP A 601 " pdb=" O5' GTP A 601 " pdb=" PA GTP A 601 " pdb=" O3A GTP A 601 " ideal model delta sinusoidal sigma weight residual 69.27 -109.97 179.24 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP F 602 " pdb=" O5' GTP F 602 " pdb=" PA GTP F 602 " pdb=" O3A GTP F 602 " ideal model delta sinusoidal sigma weight residual 69.27 -109.97 179.23 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP C 602 " pdb=" O5' GTP C 602 " pdb=" PA GTP C 602 " pdb=" O3A GTP C 602 " ideal model delta sinusoidal sigma weight residual 69.27 -109.97 179.23 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 15075 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: 0.03 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.140 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 13.440 179.239 9666 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 aren 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 covalent geometry : bond 0.01090 (24564) covalent geometry : angle 1.01652 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.29167 ( 1044) hydrogen bonds : angle 10.25956 ( 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 : 0.742 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: 0.8283 (ttm170) REVERT: A 500 PHE cc_start: 0.6644 (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: 0.8339 (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: 0.8871 (mttt) cc_final: 0.8535 (mtpp) REVERT: E 330 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7755 (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: 0.7530 (mm-40) REVERT: F 500 PHE cc_start: 0.6752 (m-10) cc_final: 0.5617 (m-80) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.1702 time to fit residues: 132.4836 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 : 0.569 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 81 GLN A 82 HIS A 85 HIS A 205 GLN A 225 ASN A 463 GLN A 484 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 494 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.103198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076115 restraints weight = 61114.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078969 restraints weight = 31508.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080763 restraints weight = 20920.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081865 restraints weight = 16435.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082512 restraints weight = 14319.059| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 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 = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24564 Z= 0.165 Angle : 0.671 6.784 33324 Z= 0.348 Chirality : 0.045 0.169 3612 Planarity : 0.005 0.037 4230 Dihedral : 16.090 170.456 4074 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.24 % Allowed : 6.29 % Favored : 91.47 % 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 aren not related in a simple way. whole: -3.20 (0.14), residues: 2964 helix: -1.59 (0.11), residues: 1458 sheet: -3.21 (0.23), residues: 324 loop : -2.30 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 439 TYR 0.023 0.002 TYR A 407 PHE 0.026 0.003 PHE B 360 TRP 0.016 0.002 TRP E 178 HIS 0.004 0.001 HIS D 408 Details of bonding type rmsd covalent geometry : bond 0.00374 (24564) covalent geometry : angle 0.67092 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.04825 ( 1044) hydrogen bonds : angle 5.57134 ( 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 449 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 393 time to evaluate : 0.773 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: 0.8574 (p0) cc_final: 0.8256 (p0) REVERT: A 143 LYS cc_start: 0.8777 (mttt) cc_final: 0.8403 (mtpp) REVERT: A 151 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8125 (mm-30) REVERT: A 181 ASP cc_start: 0.7691 (t0) cc_final: 0.7146 (t0) REVERT: B 25 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8162 (mm-30) REVERT: B 143 LYS cc_start: 0.8738 (mttt) cc_final: 0.8393 (mtpp) REVERT: B 181 ASP cc_start: 0.7536 (t0) cc_final: 0.6778 (t0) REVERT: B 233 MET cc_start: 0.7024 (tpt) cc_final: 0.6777 (tpt) REVERT: B 250 GLN cc_start: 0.8002 (tt0) cc_final: 0.6405 (tt0) REVERT: B 294 PHE cc_start: 0.8553 (m-10) cc_final: 0.8341 (m-10) REVERT: B 364 ASN cc_start: 0.7071 (t0) cc_final: 0.6858 (t0) REVERT: B 479 THR cc_start: 0.8824 (m) cc_final: 0.8519 (p) REVERT: C 84 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7795 (mp10) REVERT: C 143 LYS cc_start: 0.8781 (mttt) cc_final: 0.8386 (mtpp) REVERT: C 181 ASP cc_start: 0.7668 (t0) cc_final: 0.7202 (t0) REVERT: C 238 MET cc_start: 0.5127 (mmp) cc_final: 0.4767 (mmm) REVERT: C 250 GLN cc_start: 0.7924 (tt0) cc_final: 0.7088 (tt0) REVERT: C 294 PHE cc_start: 0.8584 (m-10) cc_final: 0.8317 (m-80) REVERT: D 102 ASP cc_start: 0.8567 (p0) cc_final: 0.8249 (p0) REVERT: D 143 LYS cc_start: 0.8773 (mttt) cc_final: 0.8405 (mtpp) REVERT: D 151 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8117 (mm-30) REVERT: D 181 ASP cc_start: 0.7627 (t0) cc_final: 0.7101 (t0) REVERT: E 25 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8167 (mm-30) REVERT: E 143 LYS cc_start: 0.8736 (mttt) cc_final: 0.8387 (mtpp) REVERT: E 181 ASP cc_start: 0.7548 (t0) cc_final: 0.7185 (t0) REVERT: E 233 MET cc_start: 0.7019 (tpt) cc_final: 0.6769 (tpt) REVERT: E 250 GLN cc_start: 0.7992 (tt0) cc_final: 0.7542 (tt0) REVERT: E 294 PHE cc_start: 0.8559 (m-10) cc_final: 0.8348 (m-10) REVERT: E 330 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6966 (mm-40) REVERT: E 364 ASN cc_start: 0.7096 (t0) cc_final: 0.6885 (t0) REVERT: E 479 THR cc_start: 0.8832 (m) cc_final: 0.8524 (p) REVERT: F 84 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7804 (mp10) REVERT: F 143 LYS cc_start: 0.8779 (mttt) cc_final: 0.8381 (mtpp) REVERT: F 181 ASP cc_start: 0.7671 (t0) cc_final: 0.7209 (t0) REVERT: F 238 MET cc_start: 0.5120 (mmp) cc_final: 0.4753 (mmm) REVERT: F 250 GLN cc_start: 0.7929 (tt0) cc_final: 0.7083 (tt0) REVERT: F 294 PHE cc_start: 0.8581 (m-10) cc_final: 0.8319 (m-80) outliers start: 56 outliers final: 42 residues processed: 423 average time/residue: 0.1502 time to fit residues: 100.9248 Evaluate side-chains 305 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 25 GLU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 112 THR 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 25 GLU Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 112 THR 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: 30.0000 chunk 126 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 79 optimal weight: 0.0570 chunk 177 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 overall best weight: 4.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 494 ASN B 85 HIS B 205 GLN B 494 ASN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN C 494 ASN D 85 HIS D 484 ASN D 494 ASN E 85 HIS E 205 GLN E 494 ASN ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3648 r_free = 0.3648 target = 0.099413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072909 restraints weight = 61341.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075657 restraints weight = 30844.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077436 restraints weight = 20321.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078503 restraints weight = 15895.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078979 restraints weight = 13850.335| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24564 Z= 0.167 Angle : 0.634 9.314 33324 Z= 0.323 Chirality : 0.044 0.174 3612 Planarity : 0.004 0.038 4230 Dihedral : 15.649 169.472 4074 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.88 % Allowed : 8.33 % Favored : 88.78 % 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 aren not related in a simple way. whole: -2.28 (0.14), residues: 2964 helix: -0.73 (0.12), residues: 1458 sheet: -2.95 (0.24), residues: 318 loop : -1.95 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 86 TYR 0.022 0.002 TYR B 407 PHE 0.018 0.002 PHE F 490 TRP 0.014 0.001 TRP A 72 HIS 0.008 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00378 (24564) covalent geometry : angle 0.63388 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.04274 ( 1044) hydrogen bonds : angle 5.03926 ( 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 374 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 302 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8618 (p0) cc_final: 0.8255 (p0) REVERT: A 143 LYS cc_start: 0.8808 (mttt) cc_final: 0.8416 (mtpp) REVERT: A 151 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 143 LYS cc_start: 0.8787 (mttt) cc_final: 0.8500 (mtpp) REVERT: B 294 PHE cc_start: 0.8575 (m-10) cc_final: 0.8357 (m-10) REVERT: B 330 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7756 (mm-40) REVERT: B 364 ASN cc_start: 0.6940 (t0) cc_final: 0.6692 (t0) REVERT: C 84 GLN cc_start: 0.8246 (mm-40) cc_final: 0.8004 (mp10) REVERT: C 143 LYS cc_start: 0.8799 (mttt) cc_final: 0.8372 (mtpp) REVERT: C 181 ASP cc_start: 0.7821 (t0) cc_final: 0.7385 (t0) REVERT: C 238 MET cc_start: 0.5010 (mmp) cc_final: 0.4762 (mmm) REVERT: C 294 PHE cc_start: 0.8647 (m-10) cc_final: 0.8367 (m-80) REVERT: C 364 ASN cc_start: 0.6886 (t0) cc_final: 0.6676 (t0) REVERT: D 102 ASP cc_start: 0.8612 (p0) cc_final: 0.8243 (p0) REVERT: D 143 LYS cc_start: 0.8804 (mttt) cc_final: 0.8428 (mtpp) REVERT: D 151 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8095 (mm-30) REVERT: E 143 LYS cc_start: 0.8766 (mttt) cc_final: 0.8389 (mtpp) REVERT: E 250 GLN cc_start: 0.7971 (tt0) cc_final: 0.7567 (tt0) REVERT: E 294 PHE cc_start: 0.8576 (m-10) cc_final: 0.8350 (m-10) REVERT: E 330 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6934 (mm-40) REVERT: E 364 ASN cc_start: 0.7003 (t0) cc_final: 0.6752 (t0) REVERT: F 84 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7996 (mp10) REVERT: F 143 LYS cc_start: 0.8800 (mttt) cc_final: 0.8354 (mtpp) REVERT: F 181 ASP cc_start: 0.7831 (t0) cc_final: 0.7398 (t0) REVERT: F 238 MET cc_start: 0.5011 (mmp) cc_final: 0.4757 (mmm) REVERT: F 294 PHE cc_start: 0.8642 (m-10) cc_final: 0.8368 (m-80) REVERT: F 364 ASN cc_start: 0.6934 (t0) cc_final: 0.6726 (t0) outliers start: 72 outliers final: 41 residues processed: 350 average time/residue: 0.1529 time to fit residues: 85.2278 Evaluate side-chains 273 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 119 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 17 PHE 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 B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 110 LEU 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 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 110 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain E residue 17 PHE 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 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 110 LEU 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 460 SER 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: 0.7980 chunk 16 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 265 optimal weight: 20.0000 chunk 134 optimal weight: 0.7980 chunk 200 optimal weight: 0.0070 chunk 12 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 overall best weight: 2.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN C 85 HIS C 484 ASN D 330 GLN F 85 HIS F 484 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.074451 restraints weight = 60973.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077250 restraints weight = 30496.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079022 restraints weight = 19956.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080108 restraints weight = 15551.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.080647 restraints weight = 13490.033| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 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 = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24564 Z= 0.120 Angle : 0.573 11.323 33324 Z= 0.289 Chirality : 0.043 0.168 3612 Planarity : 0.004 0.039 4230 Dihedral : 15.144 165.071 4074 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.00 % Allowed : 10.70 % Favored : 87.30 % 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 aren not related in a simple way. whole: -1.50 (0.15), residues: 2964 helix: -0.03 (0.13), residues: 1458 sheet: -2.34 (0.25), residues: 378 loop : -1.66 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 403 TYR 0.019 0.001 TYR A 407 PHE 0.015 0.002 PHE F 490 TRP 0.017 0.001 TRP E 72 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00267 (24564) covalent geometry : angle 0.57262 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03561 ( 1044) hydrogen bonds : angle 4.58032 ( 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 362 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 312 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.7849 (m-10) cc_final: 0.7505 (m-10) REVERT: A 102 ASP cc_start: 0.8611 (p0) cc_final: 0.8172 (p0) REVERT: A 143 LYS cc_start: 0.8827 (mttt) cc_final: 0.8438 (mtpp) REVERT: A 181 ASP cc_start: 0.8098 (t0) cc_final: 0.7765 (t0) REVERT: A 250 GLN cc_start: 0.8123 (tt0) cc_final: 0.7776 (pt0) REVERT: A 294 PHE cc_start: 0.8518 (m-10) cc_final: 0.8221 (m-80) REVERT: B 25 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8248 (mm-30) REVERT: B 143 LYS cc_start: 0.8804 (mttt) cc_final: 0.8532 (mtpp) REVERT: B 294 PHE cc_start: 0.8616 (m-10) cc_final: 0.8387 (m-10) REVERT: B 330 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7641 (mm-40) REVERT: B 364 ASN cc_start: 0.6856 (t0) cc_final: 0.6596 (t0) REVERT: B 437 GLN cc_start: 0.8305 (tp40) cc_final: 0.8048 (tp-100) REVERT: C 84 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7829 (mp10) REVERT: C 143 LYS cc_start: 0.8788 (mttt) cc_final: 0.8381 (mtpp) REVERT: C 181 ASP cc_start: 0.7885 (t0) cc_final: 0.7309 (t0) REVERT: C 250 GLN cc_start: 0.7952 (tt0) cc_final: 0.7440 (pt0) REVERT: C 294 PHE cc_start: 0.8696 (m-10) cc_final: 0.8385 (m-80) REVERT: C 437 GLN cc_start: 0.8430 (tp40) cc_final: 0.8150 (tp-100) REVERT: D 63 PHE cc_start: 0.7854 (m-10) cc_final: 0.7511 (m-10) REVERT: D 102 ASP cc_start: 0.8615 (p0) cc_final: 0.8171 (p0) REVERT: D 143 LYS cc_start: 0.8834 (mttt) cc_final: 0.8452 (mtpp) REVERT: D 232 TYR cc_start: 0.7842 (m-80) cc_final: 0.7426 (m-80) REVERT: D 250 GLN cc_start: 0.8104 (tt0) cc_final: 0.7740 (pt0) REVERT: D 294 PHE cc_start: 0.8523 (m-10) cc_final: 0.8240 (m-80) REVERT: E 25 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: E 143 LYS cc_start: 0.8796 (mttt) cc_final: 0.8524 (mtpp) REVERT: E 250 GLN cc_start: 0.7951 (tt0) cc_final: 0.6705 (tt0) REVERT: E 294 PHE cc_start: 0.8573 (m-10) cc_final: 0.8361 (m-10) REVERT: E 364 ASN cc_start: 0.6897 (t0) cc_final: 0.6651 (t0) REVERT: F 84 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7810 (mp10) REVERT: F 143 LYS cc_start: 0.8790 (mttt) cc_final: 0.8381 (mtpp) REVERT: F 181 ASP cc_start: 0.7896 (t0) cc_final: 0.7318 (t0) REVERT: F 250 GLN cc_start: 0.7930 (tt0) cc_final: 0.7426 (pt0) REVERT: F 294 PHE cc_start: 0.8687 (m-10) cc_final: 0.8399 (m-80) REVERT: F 437 GLN cc_start: 0.8410 (tp40) cc_final: 0.8151 (tp-100) outliers start: 50 outliers final: 35 residues processed: 352 average time/residue: 0.1680 time to fit residues: 92.9770 Evaluate side-chains 279 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 460 SER 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 110 LEU Chi-restraints excluded: chain C residue 173 GLU 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 D residue 17 PHE 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 236 LEU 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 110 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073210 restraints weight = 60787.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.075976 restraints weight = 30715.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077741 restraints weight = 20186.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.078834 restraints weight = 15723.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079490 restraints weight = 13613.906| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 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 = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24564 Z= 0.145 Angle : 0.578 9.256 33324 Z= 0.293 Chirality : 0.043 0.199 3612 Planarity : 0.004 0.037 4230 Dihedral : 14.841 163.913 4074 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.84 % Allowed : 10.58 % Favored : 86.58 % 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 aren not related in a simple way. whole: -1.16 (0.15), residues: 2964 helix: 0.20 (0.13), residues: 1452 sheet: -2.08 (0.25), residues: 378 loop : -1.45 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 462 TYR 0.019 0.001 TYR A 407 PHE 0.013 0.002 PHE B 220 TRP 0.011 0.001 TRP B 72 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00330 (24564) covalent geometry : angle 0.57855 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03648 ( 1044) hydrogen bonds : angle 4.44235 ( 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 322 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 251 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8621 (p0) cc_final: 0.8184 (p0) REVERT: A 143 LYS cc_start: 0.8848 (mttt) cc_final: 0.8461 (mtpp) REVERT: A 181 ASP cc_start: 0.8139 (t0) cc_final: 0.7751 (t0) REVERT: A 250 GLN cc_start: 0.8102 (tt0) cc_final: 0.7408 (pt0) REVERT: A 263 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 294 PHE cc_start: 0.8616 (m-10) cc_final: 0.8282 (m-80) REVERT: B 25 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8264 (mm-30) REVERT: B 143 LYS cc_start: 0.8826 (mttt) cc_final: 0.8550 (mtpp) REVERT: B 233 MET cc_start: 0.7221 (tpt) cc_final: 0.6855 (tpt) REVERT: B 250 GLN cc_start: 0.7908 (tt0) cc_final: 0.7235 (pt0) REVERT: B 364 ASN cc_start: 0.6910 (t0) cc_final: 0.6586 (t0) REVERT: B 435 GLU cc_start: 0.8357 (mp0) cc_final: 0.7963 (mp0) REVERT: B 437 GLN cc_start: 0.8365 (tp40) cc_final: 0.8102 (tp-100) REVERT: C 143 LYS cc_start: 0.8802 (mttt) cc_final: 0.8412 (mtpp) REVERT: C 181 ASP cc_start: 0.7884 (t0) cc_final: 0.7298 (t0) REVERT: C 233 MET cc_start: 0.7092 (tpp) cc_final: 0.6669 (tpp) REVERT: C 250 GLN cc_start: 0.7810 (tt0) cc_final: 0.7431 (pt0) REVERT: C 294 PHE cc_start: 0.8697 (m-10) cc_final: 0.8449 (m-10) REVERT: C 437 GLN cc_start: 0.8459 (tp40) cc_final: 0.8188 (tp-100) REVERT: D 102 ASP cc_start: 0.8617 (p0) cc_final: 0.8180 (p0) REVERT: D 143 LYS cc_start: 0.8842 (mttt) cc_final: 0.8463 (mtpp) REVERT: D 233 MET cc_start: 0.7417 (mmm) cc_final: 0.7154 (mmm) REVERT: D 250 GLN cc_start: 0.8075 (tt0) cc_final: 0.7738 (pt0) REVERT: D 294 PHE cc_start: 0.8568 (m-10) cc_final: 0.8267 (m-80) REVERT: E 25 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: E 143 LYS cc_start: 0.8813 (mttt) cc_final: 0.8547 (mtpp) REVERT: E 233 MET cc_start: 0.7206 (tpt) cc_final: 0.6830 (tpt) REVERT: E 271 ILE cc_start: 0.7593 (mt) cc_final: 0.7388 (mp) REVERT: E 364 ASN cc_start: 0.6939 (t0) cc_final: 0.6618 (t0) REVERT: E 437 GLN cc_start: 0.8284 (tp40) cc_final: 0.8034 (tp-100) REVERT: E 465 MET cc_start: 0.7422 (mtm) cc_final: 0.7184 (mtm) REVERT: F 143 LYS cc_start: 0.8808 (mttt) cc_final: 0.8404 (mtpp) REVERT: F 181 ASP cc_start: 0.7908 (t0) cc_final: 0.7323 (t0) REVERT: F 233 MET cc_start: 0.7132 (tpp) cc_final: 0.6738 (tpp) REVERT: F 238 MET cc_start: 0.5601 (mmp) cc_final: 0.5144 (mtt) REVERT: F 250 GLN cc_start: 0.7779 (tt0) cc_final: 0.7397 (pt0) REVERT: F 294 PHE cc_start: 0.8732 (m-10) cc_final: 0.8528 (m-10) REVERT: F 437 GLN cc_start: 0.8437 (tp40) cc_final: 0.8191 (tp-100) outliers start: 71 outliers final: 49 residues processed: 310 average time/residue: 0.1642 time to fit residues: 82.6231 Evaluate side-chains 285 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain A residue 339 VAL 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 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 110 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 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 110 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 339 VAL 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 236 LEU 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 110 LEU Chi-restraints excluded: chain F residue 173 GLU 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 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: 0.7980 chunk 265 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 210 optimal weight: 0.0270 chunk 208 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN ** 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 = 0.3669 r_free = 0.3669 target = 0.100469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.073982 restraints weight = 60751.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076752 restraints weight = 30564.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078527 restraints weight = 20028.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079616 restraints weight = 15586.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080072 restraints weight = 13524.793| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 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 = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24564 Z= 0.121 Angle : 0.561 8.428 33324 Z= 0.283 Chirality : 0.042 0.201 3612 Planarity : 0.004 0.037 4230 Dihedral : 14.340 157.599 4074 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.04 % Allowed : 11.90 % Favored : 86.06 % 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 aren not related in a simple way. whole: -0.92 (0.15), residues: 2964 helix: 0.34 (0.13), residues: 1470 sheet: -1.85 (0.25), residues: 378 loop : -1.31 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 462 TYR 0.017 0.001 TYR C 407 PHE 0.011 0.001 PHE D 490 TRP 0.013 0.001 TRP B 72 HIS 0.003 0.001 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00274 (24564) covalent geometry : angle 0.56066 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03403 ( 1044) hydrogen bonds : angle 4.33174 ( 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 310 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8603 (p0) cc_final: 0.8140 (p0) REVERT: A 119 ASP cc_start: 0.7966 (t0) cc_final: 0.7556 (t0) REVERT: A 143 LYS cc_start: 0.8831 (mttt) cc_final: 0.8444 (mtpp) REVERT: A 181 ASP cc_start: 0.8105 (t0) cc_final: 0.7657 (t0) REVERT: A 250 GLN cc_start: 0.8094 (tt0) cc_final: 0.7402 (pt0) REVERT: A 294 PHE cc_start: 0.8714 (m-10) cc_final: 0.8371 (m-80) REVERT: B 143 LYS cc_start: 0.8820 (mttt) cc_final: 0.8585 (mtpp) REVERT: B 233 MET cc_start: 0.7201 (tpt) cc_final: 0.6816 (tpt) REVERT: B 250 GLN cc_start: 0.7875 (tt0) cc_final: 0.6801 (pt0) REVERT: B 294 PHE cc_start: 0.8618 (m-10) cc_final: 0.8373 (m-10) REVERT: B 435 GLU cc_start: 0.8327 (mp0) cc_final: 0.7995 (mp0) REVERT: B 437 GLN cc_start: 0.8341 (tp40) cc_final: 0.8102 (tp-100) REVERT: C 84 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7805 (mp10) REVERT: C 119 ASP cc_start: 0.7950 (t0) cc_final: 0.7465 (t0) REVERT: C 143 LYS cc_start: 0.8810 (mttt) cc_final: 0.8442 (mtpp) REVERT: C 181 ASP cc_start: 0.7882 (t0) cc_final: 0.7408 (t70) REVERT: C 250 GLN cc_start: 0.7772 (tt0) cc_final: 0.7354 (pt0) REVERT: C 294 PHE cc_start: 0.8723 (m-10) cc_final: 0.8452 (m-10) REVERT: C 437 GLN cc_start: 0.8448 (tp40) cc_final: 0.8176 (tp-100) REVERT: D 102 ASP cc_start: 0.8604 (p0) cc_final: 0.8140 (p0) REVERT: D 143 LYS cc_start: 0.8835 (mttt) cc_final: 0.8451 (mtpp) REVERT: D 233 MET cc_start: 0.7235 (mmm) cc_final: 0.6902 (mmm) REVERT: D 250 GLN cc_start: 0.8099 (tt0) cc_final: 0.7787 (pt0) REVERT: D 294 PHE cc_start: 0.8638 (m-10) cc_final: 0.8329 (m-80) REVERT: E 143 LYS cc_start: 0.8817 (mttt) cc_final: 0.8557 (mtpp) REVERT: E 233 MET cc_start: 0.7278 (tpt) cc_final: 0.6904 (tpt) REVERT: E 294 PHE cc_start: 0.8571 (m-10) cc_final: 0.8354 (m-10) REVERT: E 437 GLN cc_start: 0.8310 (tp40) cc_final: 0.8048 (tp-100) REVERT: F 84 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7821 (mp10) REVERT: F 119 ASP cc_start: 0.7971 (t0) cc_final: 0.7464 (t0) REVERT: F 143 LYS cc_start: 0.8812 (mttt) cc_final: 0.8435 (mtpp) REVERT: F 181 ASP cc_start: 0.7892 (t0) cc_final: 0.7418 (t70) REVERT: F 250 GLN cc_start: 0.7771 (tt0) cc_final: 0.7325 (pt0) REVERT: F 294 PHE cc_start: 0.8757 (m-10) cc_final: 0.8534 (m-10) REVERT: F 437 GLN cc_start: 0.8437 (tp40) cc_final: 0.8202 (tp-100) outliers start: 51 outliers final: 43 residues processed: 302 average time/residue: 0.1636 time to fit residues: 80.4530 Evaluate side-chains 277 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 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 242 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 460 SER 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 110 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 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 460 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 236 LEU 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 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 469 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 131 optimal weight: 8.9990 chunk 272 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** 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 = 0.3629 r_free = 0.3629 target = 0.098153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.071540 restraints weight = 60836.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074257 restraints weight = 30827.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076001 restraints weight = 20289.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.077081 restraints weight = 15839.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077545 restraints weight = 13748.542| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 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 = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24564 Z= 0.196 Angle : 0.632 7.943 33324 Z= 0.319 Chirality : 0.045 0.215 3612 Planarity : 0.004 0.036 4230 Dihedral : 13.722 154.406 4074 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.17 % Allowed : 11.82 % Favored : 85.02 % 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 aren not related in a simple way. whole: -1.14 (0.15), residues: 2964 helix: 0.11 (0.13), residues: 1506 sheet: -1.85 (0.25), residues: 378 loop : -1.44 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 462 TYR 0.019 0.002 TYR E 407 PHE 0.013 0.002 PHE D 490 TRP 0.010 0.001 TRP B 72 HIS 0.005 0.001 HIS E 258 Details of bonding type rmsd covalent geometry : bond 0.00444 (24564) covalent geometry : angle 0.63240 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.04021 ( 1044) hydrogen bonds : angle 4.54463 ( 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 332 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 253 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8638 (p0) cc_final: 0.8251 (p0) REVERT: A 119 ASP cc_start: 0.8040 (t0) cc_final: 0.7619 (t0) REVERT: A 143 LYS cc_start: 0.8826 (mttt) cc_final: 0.8420 (mtpp) REVERT: A 181 ASP cc_start: 0.8057 (t0) cc_final: 0.7571 (t0) REVERT: B 25 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: B 143 LYS cc_start: 0.8868 (mttt) cc_final: 0.8583 (mtpp) REVERT: B 233 MET cc_start: 0.7249 (tpt) cc_final: 0.6880 (tpt) REVERT: B 435 GLU cc_start: 0.8353 (mp0) cc_final: 0.8073 (mp0) REVERT: B 437 GLN cc_start: 0.8391 (tp40) cc_final: 0.8165 (tp-100) REVERT: B 465 MET cc_start: 0.7371 (mtm) cc_final: 0.7095 (mtm) REVERT: C 119 ASP cc_start: 0.8050 (t0) cc_final: 0.7522 (t0) REVERT: C 143 LYS cc_start: 0.8807 (mttt) cc_final: 0.8433 (mtpp) REVERT: C 181 ASP cc_start: 0.7881 (t0) cc_final: 0.7381 (t70) REVERT: C 250 GLN cc_start: 0.7838 (tt0) cc_final: 0.6871 (pt0) REVERT: C 260 MET cc_start: 0.8479 (tmm) cc_final: 0.7613 (ptm) REVERT: C 294 PHE cc_start: 0.8800 (m-10) cc_final: 0.8554 (m-10) REVERT: C 330 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7650 (mt0) REVERT: C 437 GLN cc_start: 0.8451 (tp40) cc_final: 0.8198 (tp-100) REVERT: D 102 ASP cc_start: 0.8645 (p0) cc_final: 0.8250 (p0) REVERT: D 119 ASP cc_start: 0.8058 (t0) cc_final: 0.7629 (t0) REVERT: D 143 LYS cc_start: 0.8830 (mttt) cc_final: 0.8425 (mtpp) REVERT: D 233 MET cc_start: 0.7192 (mmm) cc_final: 0.6795 (mmm) REVERT: D 294 PHE cc_start: 0.8765 (m-10) cc_final: 0.8413 (m-80) REVERT: E 25 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8297 (mm-30) REVERT: E 143 LYS cc_start: 0.8825 (mttt) cc_final: 0.8315 (mtpp) REVERT: E 233 MET cc_start: 0.7284 (tpt) cc_final: 0.6916 (tpt) REVERT: E 294 PHE cc_start: 0.8673 (m-10) cc_final: 0.8390 (m-80) REVERT: E 295 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8325 (mttt) REVERT: E 437 GLN cc_start: 0.8387 (tp40) cc_final: 0.8146 (tp-100) REVERT: E 465 MET cc_start: 0.7381 (mtm) cc_final: 0.7093 (mtm) REVERT: F 119 ASP cc_start: 0.8086 (t0) cc_final: 0.7548 (t0) REVERT: F 143 LYS cc_start: 0.8822 (mttt) cc_final: 0.8428 (mtpp) REVERT: F 181 ASP cc_start: 0.7886 (t0) cc_final: 0.7400 (t70) REVERT: F 250 GLN cc_start: 0.7821 (tt0) cc_final: 0.6869 (pt0) REVERT: F 260 MET cc_start: 0.8519 (tmm) cc_final: 0.7656 (ptm) REVERT: F 294 PHE cc_start: 0.8862 (m-10) cc_final: 0.8637 (m-10) REVERT: F 330 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7676 (mt0) REVERT: F 437 GLN cc_start: 0.8462 (tp40) cc_final: 0.8248 (tp-100) outliers start: 79 outliers final: 68 residues processed: 313 average time/residue: 0.1520 time to fit residues: 78.4425 Evaluate side-chains 304 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 234 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 460 SER 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 138 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 236 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 B residue 475 LEU Chi-restraints excluded: chain B residue 479 THR 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 110 LEU Chi-restraints excluded: chain C residue 191 ASP 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 499 THR 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 191 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 263 LEU 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 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 191 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 413 VAL 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 479 THR 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 110 LEU Chi-restraints excluded: chain F residue 191 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 2 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN D 258 HIS E 258 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 GLN ** F 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073190 restraints weight = 60396.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.075903 restraints weight = 30446.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077676 restraints weight = 20077.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078765 restraints weight = 15679.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079392 restraints weight = 13636.178| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24564 Z= 0.133 Angle : 0.585 8.674 33324 Z= 0.295 Chirality : 0.043 0.200 3612 Planarity : 0.004 0.039 4230 Dihedral : 13.001 177.203 4074 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.68 % Allowed : 13.22 % 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 aren not related in a simple way. whole: -0.88 (0.15), residues: 2964 helix: 0.27 (0.13), residues: 1506 sheet: -1.66 (0.25), residues: 378 loop : -1.26 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 462 TYR 0.015 0.001 TYR E 407 PHE 0.011 0.001 PHE A 490 TRP 0.012 0.001 TRP E 72 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00305 (24564) covalent geometry : angle 0.58478 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03508 ( 1044) hydrogen bonds : angle 4.35752 ( 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 321 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 254 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8596 (p0) cc_final: 0.8166 (p0) REVERT: A 119 ASP cc_start: 0.7985 (t0) cc_final: 0.7575 (t0) REVERT: A 143 LYS cc_start: 0.8839 (mttt) cc_final: 0.8445 (mtpp) REVERT: A 181 ASP cc_start: 0.8078 (t0) cc_final: 0.7631 (t0) REVERT: A 232 TYR cc_start: 0.7646 (m-10) cc_final: 0.5500 (m-10) REVERT: A 250 GLN cc_start: 0.8348 (tt0) cc_final: 0.7592 (pt0) REVERT: B 25 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8266 (mm-30) REVERT: B 143 LYS cc_start: 0.8870 (mttt) cc_final: 0.8569 (mtpp) REVERT: B 292 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7407 (pp20) REVERT: B 435 GLU cc_start: 0.8312 (mp0) cc_final: 0.8050 (mp0) REVERT: B 437 GLN cc_start: 0.8363 (tp40) cc_final: 0.8067 (tp-100) REVERT: C 119 ASP cc_start: 0.8004 (t0) cc_final: 0.7542 (t0) REVERT: C 143 LYS cc_start: 0.8807 (mttt) cc_final: 0.8462 (mtpp) REVERT: C 181 ASP cc_start: 0.7864 (t0) cc_final: 0.7379 (t70) REVERT: C 233 MET cc_start: 0.7902 (tpp) cc_final: 0.7511 (tpt) REVERT: C 250 GLN cc_start: 0.7779 (tt0) cc_final: 0.6934 (pt0) REVERT: C 260 MET cc_start: 0.8486 (tmm) cc_final: 0.7619 (ptm) REVERT: C 294 PHE cc_start: 0.8776 (m-10) cc_final: 0.8539 (m-10) REVERT: C 330 GLN cc_start: 0.7882 (mm110) cc_final: 0.7654 (mt0) REVERT: C 437 GLN cc_start: 0.8448 (tp40) cc_final: 0.8216 (tp-100) REVERT: D 102 ASP cc_start: 0.8604 (p0) cc_final: 0.8164 (p0) REVERT: D 119 ASP cc_start: 0.8004 (t0) cc_final: 0.7556 (t0) REVERT: D 143 LYS cc_start: 0.8847 (mttt) cc_final: 0.8457 (mtpp) REVERT: D 250 GLN cc_start: 0.8368 (tt0) cc_final: 0.7725 (pt0) REVERT: D 294 PHE cc_start: 0.8771 (m-10) cc_final: 0.8458 (m-80) REVERT: E 25 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8272 (mm-30) REVERT: E 143 LYS cc_start: 0.8863 (mttt) cc_final: 0.8562 (mtpp) REVERT: E 250 GLN cc_start: 0.7716 (tt0) cc_final: 0.7490 (pt0) REVERT: E 294 PHE cc_start: 0.8685 (m-10) cc_final: 0.8434 (m-80) REVERT: E 295 LYS cc_start: 0.8619 (ttpp) cc_final: 0.8308 (mttt) REVERT: E 437 GLN cc_start: 0.8341 (tp40) cc_final: 0.8107 (tp-100) REVERT: E 465 MET cc_start: 0.7372 (mtm) cc_final: 0.7112 (mtm) REVERT: F 119 ASP cc_start: 0.8014 (t0) cc_final: 0.7534 (t0) REVERT: F 143 LYS cc_start: 0.8826 (mttt) cc_final: 0.8440 (mtpp) REVERT: F 181 ASP cc_start: 0.7840 (t0) cc_final: 0.7355 (t0) REVERT: F 250 GLN cc_start: 0.7762 (tt0) cc_final: 0.6922 (pt0) REVERT: F 260 MET cc_start: 0.8515 (tmm) cc_final: 0.7643 (ptm) REVERT: F 294 PHE cc_start: 0.8818 (m-10) cc_final: 0.8611 (m-10) REVERT: F 330 GLN cc_start: 0.7876 (mm110) cc_final: 0.7654 (mt0) outliers start: 67 outliers final: 50 residues processed: 311 average time/residue: 0.1436 time to fit residues: 74.5737 Evaluate side-chains 296 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 460 SER 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 236 LEU 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 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 110 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 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 110 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 460 SER 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 236 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 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 110 LEU 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 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 499 THR 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: 10.0000 chunk 172 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 HIS ** 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 = 0.3629 r_free = 0.3629 target = 0.098175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071461 restraints weight = 60808.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074142 restraints weight = 30879.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075850 restraints weight = 20442.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076913 restraints weight = 16070.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077360 restraints weight = 14005.186| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 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 = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24564 Z= 0.211 Angle : 0.643 10.005 33324 Z= 0.326 Chirality : 0.045 0.217 3612 Planarity : 0.004 0.039 4230 Dihedral : 12.448 174.048 4074 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.96 % Allowed : 13.42 % Favored : 83.61 % 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 aren not related in a simple way. whole: -1.00 (0.15), residues: 2964 helix: 0.18 (0.13), residues: 1488 sheet: -1.70 (0.24), residues: 378 loop : -1.31 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.024 0.002 TYR A 232 PHE 0.013 0.002 PHE A 490 TRP 0.006 0.001 TRP C 72 HIS 0.004 0.001 HIS F 258 Details of bonding type rmsd covalent geometry : bond 0.00476 (24564) covalent geometry : angle 0.64292 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03982 ( 1044) hydrogen bonds : angle 4.57828 ( 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 330 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 256 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8649 (p0) cc_final: 0.8260 (p0) REVERT: A 119 ASP cc_start: 0.8083 (t0) cc_final: 0.7664 (t0) REVERT: A 143 LYS cc_start: 0.8846 (mttt) cc_final: 0.8431 (mtpp) REVERT: A 181 ASP cc_start: 0.8079 (t0) cc_final: 0.7644 (t0) REVERT: A 233 MET cc_start: 0.7123 (mmm) cc_final: 0.6882 (mmt) REVERT: A 250 GLN cc_start: 0.8366 (tt0) cc_final: 0.7646 (pt0) REVERT: B 143 LYS cc_start: 0.8884 (mttt) cc_final: 0.8561 (mtpp) REVERT: B 437 GLN cc_start: 0.8389 (tp40) cc_final: 0.8100 (tp-100) REVERT: C 119 ASP cc_start: 0.8106 (t0) cc_final: 0.7603 (t0) REVERT: C 143 LYS cc_start: 0.8823 (mttt) cc_final: 0.8459 (mtpp) REVERT: C 181 ASP cc_start: 0.7865 (t0) cc_final: 0.7373 (t70) REVERT: C 233 MET cc_start: 0.7910 (tpp) cc_final: 0.7513 (tpt) REVERT: C 250 GLN cc_start: 0.7879 (tt0) cc_final: 0.7138 (pt0) REVERT: C 260 MET cc_start: 0.8532 (tmm) cc_final: 0.7551 (ptm) REVERT: C 294 PHE cc_start: 0.8810 (m-10) cc_final: 0.8569 (m-10) REVERT: C 330 GLN cc_start: 0.7903 (mm110) cc_final: 0.7539 (mt0) REVERT: C 437 GLN cc_start: 0.8464 (tp40) cc_final: 0.8237 (tp-100) REVERT: D 102 ASP cc_start: 0.8651 (p0) cc_final: 0.8259 (p0) REVERT: D 119 ASP cc_start: 0.8077 (t0) cc_final: 0.7634 (t0) REVERT: D 143 LYS cc_start: 0.8856 (mttt) cc_final: 0.8443 (mtpp) REVERT: D 232 TYR cc_start: 0.7674 (m-10) cc_final: 0.5979 (m-10) REVERT: D 250 GLN cc_start: 0.8355 (tt0) cc_final: 0.7633 (pt0) REVERT: D 294 PHE cc_start: 0.8822 (m-10) cc_final: 0.8505 (m-80) REVERT: E 143 LYS cc_start: 0.8889 (mttt) cc_final: 0.8555 (mtpp) REVERT: E 250 GLN cc_start: 0.7740 (tt0) cc_final: 0.7508 (pt0) REVERT: E 294 PHE cc_start: 0.8754 (m-10) cc_final: 0.8492 (m-80) REVERT: E 435 GLU cc_start: 0.8381 (mp0) cc_final: 0.7978 (mp0) REVERT: E 437 GLN cc_start: 0.8408 (tp40) cc_final: 0.8195 (tp-100) REVERT: E 465 MET cc_start: 0.7341 (mtm) cc_final: 0.7108 (mtm) REVERT: F 119 ASP cc_start: 0.8120 (t0) cc_final: 0.7788 (t0) REVERT: F 143 LYS cc_start: 0.8821 (mttt) cc_final: 0.8438 (mtpp) REVERT: F 181 ASP cc_start: 0.7840 (t0) cc_final: 0.7462 (t70) REVERT: F 233 MET cc_start: 0.7615 (tpp) cc_final: 0.7367 (tpp) REVERT: F 250 GLN cc_start: 0.7839 (tt0) cc_final: 0.6980 (pt0) REVERT: F 260 MET cc_start: 0.8513 (tmm) cc_final: 0.7675 (ptm) REVERT: F 294 PHE cc_start: 0.8858 (m-10) cc_final: 0.8639 (m-10) REVERT: F 330 GLN cc_start: 0.7903 (mm110) cc_final: 0.7662 (mt0) outliers start: 74 outliers final: 61 residues processed: 313 average time/residue: 0.1506 time to fit residues: 77.1560 Evaluate side-chains 310 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 499 THR Chi-restraints excluded: chain B residue 17 PHE 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 235 ILE Chi-restraints excluded: chain B residue 236 LEU 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 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 110 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 ILE 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 110 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 263 LEU 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 499 THR Chi-restraints excluded: chain E residue 17 PHE 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 236 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 110 LEU 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 469 MET Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 45 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 38 optimal weight: 0.0170 overall best weight: 2.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 HIS ** 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 = 0.3657 r_free = 0.3657 target = 0.099851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073436 restraints weight = 60524.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076145 restraints weight = 30440.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.077917 restraints weight = 20113.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078985 restraints weight = 15733.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079616 restraints weight = 13702.681| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24564 Z= 0.129 Angle : 0.583 7.921 33324 Z= 0.297 Chirality : 0.043 0.200 3612 Planarity : 0.004 0.039 4230 Dihedral : 12.215 178.216 4074 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.20 % Allowed : 13.78 % Favored : 84.01 % 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 aren not related in a simple way. whole: -0.76 (0.15), residues: 2964 helix: 0.35 (0.13), residues: 1488 sheet: -1.58 (0.25), residues: 378 loop : -1.16 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 466 TYR 0.019 0.001 TYR D 232 PHE 0.013 0.001 PHE D 500 TRP 0.008 0.001 TRP E 72 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00297 (24564) covalent geometry : angle 0.58277 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03468 ( 1044) hydrogen bonds : angle 4.36950 ( 2934) ********************** REFINEMENT MACRO_CYCLE 10 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 308 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8592 (p0) cc_final: 0.8154 (p0) REVERT: A 119 ASP cc_start: 0.7970 (t0) cc_final: 0.7585 (t0) REVERT: A 143 LYS cc_start: 0.8837 (mttt) cc_final: 0.8435 (mtpp) REVERT: A 181 ASP cc_start: 0.8070 (t0) cc_final: 0.7729 (t0) REVERT: A 250 GLN cc_start: 0.8351 (tt0) cc_final: 0.7718 (pt0) REVERT: B 143 LYS cc_start: 0.8875 (mttt) cc_final: 0.8567 (mtpp) REVERT: B 233 MET cc_start: 0.7256 (tpt) cc_final: 0.6992 (tpp) REVERT: B 292 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7388 (pp20) REVERT: B 435 GLU cc_start: 0.8333 (mp0) cc_final: 0.7936 (mp0) REVERT: C 119 ASP cc_start: 0.8005 (t0) cc_final: 0.7546 (t0) REVERT: C 143 LYS cc_start: 0.8819 (mttt) cc_final: 0.8497 (mtpp) REVERT: C 181 ASP cc_start: 0.7858 (t0) cc_final: 0.7367 (t70) REVERT: C 233 MET cc_start: 0.7800 (tpp) cc_final: 0.7358 (tpt) REVERT: C 250 GLN cc_start: 0.7818 (tt0) cc_final: 0.6810 (pt0) REVERT: C 260 MET cc_start: 0.8498 (tmm) cc_final: 0.7556 (ptm) REVERT: C 294 PHE cc_start: 0.8776 (m-10) cc_final: 0.8559 (m-10) REVERT: C 330 GLN cc_start: 0.7862 (mm110) cc_final: 0.7556 (mt0) REVERT: C 437 GLN cc_start: 0.8439 (tp40) cc_final: 0.8232 (tp-100) REVERT: D 102 ASP cc_start: 0.8612 (p0) cc_final: 0.8164 (p0) REVERT: D 119 ASP cc_start: 0.7997 (t0) cc_final: 0.7573 (t0) REVERT: D 143 LYS cc_start: 0.8843 (mttt) cc_final: 0.8437 (mtpp) REVERT: D 250 GLN cc_start: 0.8372 (tt0) cc_final: 0.7756 (pt0) REVERT: D 294 PHE cc_start: 0.8814 (m-10) cc_final: 0.8506 (m-80) REVERT: E 143 LYS cc_start: 0.8877 (mttt) cc_final: 0.8563 (mtpp) REVERT: E 233 MET cc_start: 0.7336 (tpt) cc_final: 0.7068 (tpp) REVERT: E 250 GLN cc_start: 0.7804 (tt0) cc_final: 0.7316 (pt0) REVERT: E 294 PHE cc_start: 0.8711 (m-10) cc_final: 0.8474 (m-80) REVERT: E 435 GLU cc_start: 0.8369 (mp0) cc_final: 0.7959 (mp0) REVERT: E 437 GLN cc_start: 0.8370 (tp40) cc_final: 0.8152 (tp-100) REVERT: F 119 ASP cc_start: 0.8033 (t0) cc_final: 0.7558 (t0) REVERT: F 143 LYS cc_start: 0.8833 (mttt) cc_final: 0.8523 (mtpp) REVERT: F 181 ASP cc_start: 0.7827 (t0) cc_final: 0.7383 (t70) REVERT: F 250 GLN cc_start: 0.7768 (tt0) cc_final: 0.7083 (pt0) REVERT: F 260 MET cc_start: 0.8494 (tmm) cc_final: 0.7586 (ptm) REVERT: F 330 GLN cc_start: 0.7867 (mm110) cc_final: 0.7539 (mt0) REVERT: F 407 TYR cc_start: 0.7711 (p90) cc_final: 0.7505 (p90) outliers start: 55 outliers final: 48 residues processed: 298 average time/residue: 0.1404 time to fit residues: 70.0440 Evaluate side-chains 287 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 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 192 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE 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 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 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 110 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 469 MET 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 192 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE 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 339 VAL Chi-restraints excluded: chain E residue 373 LEU 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 110 LEU Chi-restraints excluded: chain F residue 242 PHE 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 469 MET Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 94 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073674 restraints weight = 60124.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.076407 restraints weight = 30332.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078153 restraints weight = 19980.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079227 restraints weight = 15650.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.079843 restraints weight = 13633.288| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24564 Z= 0.129 Angle : 0.584 7.870 33324 Z= 0.296 Chirality : 0.043 0.202 3612 Planarity : 0.004 0.039 4230 Dihedral : 11.944 179.671 4074 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.88 % Allowed : 14.38 % Favored : 83.73 % 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 aren not related in a simple way. whole: -0.66 (0.15), residues: 2964 helix: 0.45 (0.13), residues: 1488 sheet: -1.51 (0.25), residues: 378 loop : -1.13 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 462 TYR 0.014 0.001 TYR C 407 PHE 0.012 0.001 PHE D 500 TRP 0.008 0.001 TRP C 72 HIS 0.003 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00297 (24564) covalent geometry : angle 0.58454 (33318) SS BOND : angle 0.00000 ( 6) hydrogen bonds : bond 0.03442 ( 1044) hydrogen bonds : angle 4.32599 ( 2934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4110.30 seconds wall clock time: 72 minutes 11.02 seconds (4331.02 seconds total)