Starting phenix.real_space_refine on Fri Jun 20 09:40:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd3_6632/06_2025/3jd3_6632.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd3_6632/06_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_6632/06_2025/3jd3_6632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd3_6632/06_2025/3jd3_6632.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd3_6632/06_2025/3jd3_6632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd3_6632/06_2025/3jd3_6632.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.65, per 1000 atoms: 0.65 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: 6.28 Conformation dependent library (CDL) restraints added in 2.8 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 27 sheets defined 55.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 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: 7.73 Time building geometry restraints manager: 7.37 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: 0.04 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.930 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.070 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.310 ------------------------------------------------------------------------------- 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 : 18.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.004 TRP A 281 HIS 0.009 0.002 HIS C 189 PHE 0.019 0.003 PHE B 490 TYR 0.024 0.003 TYR F 262 ARG 0.006 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.29167 ( 1044) hydrogen bonds : angle 10.25956 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.01090 (24564) covalent geometry : angle 1.01652 (33318) *********************** 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 : 2.831 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: 0.4028 time to fit residues: 310.6550 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 : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 463 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN B 56 ASN B 81 GLN B 82 HIS B 85 HIS B 193 ASN ** 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 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 193 ASN ** 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: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.101601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074477 restraints weight = 61038.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077261 restraints weight = 31632.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079028 restraints weight = 21126.282| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24564 Z= 0.212 Angle : 0.713 7.044 33324 Z= 0.369 Chirality : 0.046 0.172 3612 Planarity : 0.005 0.041 4230 Dihedral : 16.217 173.173 4074 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.24 % Allowed : 6.93 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.14), residues: 2964 helix: -1.78 (0.11), residues: 1470 sheet: -3.19 (0.23), residues: 324 loop : -2.44 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 178 HIS 0.005 0.001 HIS B 258 PHE 0.024 0.003 PHE A 490 TYR 0.027 0.002 TYR A 407 ARG 0.003 0.000 ARG D 439 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 1044) hydrogen bonds : angle 5.74925 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00484 (24564) covalent geometry : angle 0.71284 (33318) *********************** 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 423 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 367 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8577 (p0) cc_final: 0.8300 (p0) REVERT: A 143 LYS cc_start: 0.8800 (mttt) cc_final: 0.8397 (mtpp) REVERT: B 25 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8187 (mm-30) REVERT: B 143 LYS cc_start: 0.8744 (mttt) cc_final: 0.8418 (mtpp) REVERT: B 233 MET cc_start: 0.7038 (tpt) cc_final: 0.6673 (tpt) REVERT: B 250 GLN cc_start: 0.7974 (tt0) cc_final: 0.6369 (tt0) REVERT: B 294 PHE cc_start: 0.8620 (m-10) cc_final: 0.8362 (m-10) REVERT: C 84 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7810 (mp10) REVERT: C 143 LYS cc_start: 0.8824 (mttt) cc_final: 0.8383 (mtpp) REVERT: C 181 ASP cc_start: 0.7699 (t0) cc_final: 0.7433 (t0) REVERT: C 250 GLN cc_start: 0.7956 (tt0) cc_final: 0.6997 (tt0) REVERT: C 294 PHE cc_start: 0.8624 (m-10) cc_final: 0.8349 (m-80) REVERT: D 143 LYS cc_start: 0.8796 (mttt) cc_final: 0.8399 (mtpp) REVERT: E 25 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: E 143 LYS cc_start: 0.8744 (mttt) cc_final: 0.8418 (mtpp) REVERT: E 233 MET cc_start: 0.7022 (tpt) cc_final: 0.6652 (tpt) REVERT: E 250 GLN cc_start: 0.7990 (tt0) cc_final: 0.6396 (tt0) REVERT: E 294 PHE cc_start: 0.8616 (m-10) cc_final: 0.8364 (m-10) REVERT: F 84 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7805 (mp10) REVERT: F 143 LYS cc_start: 0.8826 (mttt) cc_final: 0.8382 (mtpp) REVERT: F 181 ASP cc_start: 0.7691 (t0) cc_final: 0.7433 (t0) REVERT: F 250 GLN cc_start: 0.7950 (tt0) cc_final: 0.6997 (tt0) REVERT: F 294 PHE cc_start: 0.8628 (m-10) cc_final: 0.8354 (m-80) outliers start: 56 outliers final: 42 residues processed: 397 average time/residue: 0.3502 time to fit residues: 219.9319 Evaluate side-chains 308 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 2.975 ------------------------------------------------------------------------------- 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 191 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 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 191 ASP Chi-restraints excluded: chain E residue 236 LEU 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 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 3 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 276 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN A 494 ASN B 205 GLN B 494 ASN C 85 HIS C 205 GLN C 484 ASN C 494 ASN D 85 HIS D 205 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 ASN D 494 ASN E 205 GLN E 494 ASN F 85 HIS F 484 ASN F 494 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.075142 restraints weight = 60656.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077972 restraints weight = 30440.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079782 restraints weight = 19955.177| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3571 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= 0.117 Angle : 0.611 11.056 33324 Z= 0.310 Chirality : 0.043 0.179 3612 Planarity : 0.004 0.039 4230 Dihedral : 15.575 167.083 4074 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.16 % Allowed : 8.53 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.15), residues: 2964 helix: -0.61 (0.12), residues: 1476 sheet: -2.84 (0.24), residues: 318 loop : -1.85 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 72 HIS 0.011 0.001 HIS B 85 PHE 0.019 0.002 PHE B 360 TYR 0.020 0.001 TYR A 407 ARG 0.007 0.000 ARG F 86 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 1044) hydrogen bonds : angle 4.90713 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00251 (24564) covalent geometry : angle 0.61097 (33318) *********************** 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 396 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 342 time to evaluate : 2.648 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: A 102 ASP cc_start: 0.8624 (p0) cc_final: 0.8210 (p0) REVERT: A 143 LYS cc_start: 0.8825 (mttt) cc_final: 0.8492 (mtpp) REVERT: A 250 GLN cc_start: 0.7841 (tt0) cc_final: 0.7627 (pt0) REVERT: A 294 PHE cc_start: 0.8491 (m-10) cc_final: 0.8289 (m-10) REVERT: B 143 LYS cc_start: 0.8819 (mttt) cc_final: 0.8464 (mtpp) REVERT: B 181 ASP cc_start: 0.7907 (t0) cc_final: 0.7643 (t0) REVERT: B 233 MET cc_start: 0.7164 (tpt) cc_final: 0.6953 (tpt) REVERT: B 294 PHE cc_start: 0.8584 (m-10) cc_final: 0.8360 (m-10) REVERT: B 330 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7733 (mm-40) REVERT: C 84 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7931 (mp10) REVERT: C 143 LYS cc_start: 0.8804 (mttt) cc_final: 0.8384 (mtpp) REVERT: C 181 ASP cc_start: 0.7804 (t0) cc_final: 0.7399 (t0) REVERT: C 233 MET cc_start: 0.7303 (mmm) cc_final: 0.6980 (tpt) REVERT: C 294 PHE cc_start: 0.8691 (m-10) cc_final: 0.8429 (m-80) REVERT: C 330 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7555 (mm-40) REVERT: D 102 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8068 (p0) REVERT: D 143 LYS cc_start: 0.8821 (mttt) cc_final: 0.8496 (mtpp) REVERT: D 233 MET cc_start: 0.7637 (mmt) cc_final: 0.7271 (mmm) REVERT: D 263 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8268 (mp) REVERT: E 143 LYS cc_start: 0.8818 (mttt) cc_final: 0.8463 (mtpp) REVERT: E 181 ASP cc_start: 0.7927 (t0) cc_final: 0.7657 (t0) REVERT: E 233 MET cc_start: 0.7159 (tpt) cc_final: 0.6947 (tpt) REVERT: E 294 PHE cc_start: 0.8578 (m-10) cc_final: 0.8357 (m-10) REVERT: E 330 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7724 (mm-40) REVERT: F 84 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7911 (mp10) REVERT: F 143 LYS cc_start: 0.8806 (mttt) cc_final: 0.8383 (mtpp) REVERT: F 181 ASP cc_start: 0.7819 (t0) cc_final: 0.7391 (t0) REVERT: F 233 MET cc_start: 0.7288 (mmm) cc_final: 0.6959 (tpt) REVERT: F 294 PHE cc_start: 0.8628 (m-10) cc_final: 0.8393 (m-80) REVERT: F 330 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7562 (mm-40) REVERT: F 437 GLN cc_start: 0.8422 (tp40) cc_final: 0.8116 (tp-100) outliers start: 54 outliers final: 31 residues processed: 385 average time/residue: 0.3590 time to fit residues: 214.6567 Evaluate side-chains 277 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 112 THR 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 112 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 263 LEU 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 112 THR Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 475 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 113 optimal weight: 0.1980 chunk 114 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 272 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 70 optimal weight: 0.0670 overall best weight: 3.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN ** D 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.099847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073404 restraints weight = 61332.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076176 restraints weight = 30811.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077951 restraints weight = 20207.383| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24564 Z= 0.140 Angle : 0.591 10.019 33324 Z= 0.299 Chirality : 0.043 0.172 3612 Planarity : 0.004 0.038 4230 Dihedral : 15.217 166.697 4074 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.00 % Allowed : 10.14 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 2964 helix: -0.14 (0.13), residues: 1482 sheet: -2.58 (0.24), residues: 318 loop : -1.65 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 72 HIS 0.004 0.001 HIS E 298 PHE 0.015 0.002 PHE A 490 TYR 0.020 0.001 TYR A 407 ARG 0.005 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 1044) hydrogen bonds : angle 4.65220 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00317 (24564) covalent geometry : angle 0.59079 (33318) *********************** 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 325 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8664 (p0) cc_final: 0.8229 (p0) REVERT: A 143 LYS cc_start: 0.8844 (mttt) cc_final: 0.8510 (mtpp) REVERT: A 250 GLN cc_start: 0.7551 (tt0) cc_final: 0.7182 (pt0) REVERT: A 294 PHE cc_start: 0.8584 (m-10) cc_final: 0.8271 (m-80) REVERT: B 143 LYS cc_start: 0.8850 (mttt) cc_final: 0.8518 (mtpp) REVERT: B 181 ASP cc_start: 0.7955 (t0) cc_final: 0.7560 (t0) REVERT: B 232 TYR cc_start: 0.7581 (m-10) cc_final: 0.5046 (m-80) REVERT: B 437 GLN cc_start: 0.8354 (tp40) cc_final: 0.8090 (tp-100) REVERT: C 143 LYS cc_start: 0.8816 (mttt) cc_final: 0.8391 (mtpp) REVERT: C 181 ASP cc_start: 0.7905 (t0) cc_final: 0.7318 (t0) REVERT: C 233 MET cc_start: 0.7457 (mmm) cc_final: 0.7208 (tpt) REVERT: C 250 GLN cc_start: 0.7943 (tt0) cc_final: 0.6584 (pt0) REVERT: C 294 PHE cc_start: 0.8773 (m-10) cc_final: 0.8573 (m-10) REVERT: C 437 GLN cc_start: 0.8448 (tp40) cc_final: 0.8162 (tp-100) REVERT: D 143 LYS cc_start: 0.8845 (mttt) cc_final: 0.8517 (mtpp) REVERT: D 263 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8297 (mp) REVERT: E 25 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8253 (mm-30) REVERT: E 143 LYS cc_start: 0.8858 (mttt) cc_final: 0.8523 (mtpp) REVERT: E 181 ASP cc_start: 0.7965 (t0) cc_final: 0.7577 (t0) REVERT: F 143 LYS cc_start: 0.8822 (mttt) cc_final: 0.8392 (mtpp) REVERT: F 181 ASP cc_start: 0.7894 (t0) cc_final: 0.7304 (t0) REVERT: F 233 MET cc_start: 0.7392 (mmm) cc_final: 0.7126 (tpt) REVERT: F 250 GLN cc_start: 0.8000 (tt0) cc_final: 0.7587 (pt0) outliers start: 50 outliers final: 39 residues processed: 311 average time/residue: 0.4981 time to fit residues: 252.0909 Evaluate side-chains 272 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 2.630 ------------------------------------------------------------------------------- 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 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 191 ASP 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 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 173 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 SER 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 242 PHE Chi-restraints excluded: chain D residue 263 LEU 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 191 ASP Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 327 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 38 optimal weight: 0.0070 chunk 191 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3658 r_free = 0.3658 target = 0.099811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073342 restraints weight = 60988.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076124 restraints weight = 30610.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077919 restraints weight = 20017.541| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24564 Z= 0.134 Angle : 0.578 9.535 33324 Z= 0.291 Chirality : 0.043 0.152 3612 Planarity : 0.004 0.038 4230 Dihedral : 14.831 163.915 4074 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.60 % Allowed : 9.98 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 2964 helix: 0.09 (0.13), residues: 1494 sheet: -2.03 (0.25), residues: 378 loop : -1.37 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 72 HIS 0.004 0.001 HIS E 57 PHE 0.013 0.001 PHE A 490 TYR 0.019 0.001 TYR C 407 ARG 0.004 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 1044) hydrogen bonds : angle 4.46243 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00305 (24564) covalent geometry : angle 0.57853 (33318) *********************** 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 329 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8684 (p0) cc_final: 0.8222 (p0) REVERT: A 143 LYS cc_start: 0.8844 (mttt) cc_final: 0.8439 (mtpp) REVERT: A 294 PHE cc_start: 0.8676 (m-10) cc_final: 0.8335 (m-80) REVERT: B 25 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: B 119 ASP cc_start: 0.8057 (t0) cc_final: 0.7630 (t0) REVERT: B 143 LYS cc_start: 0.8865 (mttt) cc_final: 0.8551 (mtpp) REVERT: B 181 ASP cc_start: 0.7984 (t0) cc_final: 0.7544 (t0) REVERT: B 250 GLN cc_start: 0.8125 (tt0) cc_final: 0.7560 (pt0) REVERT: B 294 PHE cc_start: 0.8617 (m-10) cc_final: 0.8337 (m-10) REVERT: B 364 ASN cc_start: 0.6946 (t0) cc_final: 0.6718 (t0) REVERT: B 435 GLU cc_start: 0.8365 (mp0) cc_final: 0.7998 (mp0) REVERT: B 437 GLN cc_start: 0.8383 (tp40) cc_final: 0.8139 (tp-100) REVERT: C 119 ASP cc_start: 0.7985 (t0) cc_final: 0.7495 (t0) REVERT: C 143 LYS cc_start: 0.8806 (mttt) cc_final: 0.8406 (mtpp) REVERT: C 181 ASP cc_start: 0.7909 (t0) cc_final: 0.7301 (t0) REVERT: C 294 PHE cc_start: 0.8799 (m-10) cc_final: 0.8585 (m-10) REVERT: C 330 GLN cc_start: 0.7896 (mt0) cc_final: 0.7641 (tt0) REVERT: C 437 GLN cc_start: 0.8486 (tp40) cc_final: 0.8201 (tp-100) REVERT: D 102 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8069 (p0) REVERT: D 143 LYS cc_start: 0.8844 (mttt) cc_final: 0.8444 (mtpp) REVERT: D 233 MET cc_start: 0.7746 (mmt) cc_final: 0.7358 (mmm) REVERT: E 143 LYS cc_start: 0.8859 (mttt) cc_final: 0.8548 (mtpp) REVERT: E 181 ASP cc_start: 0.7996 (t0) cc_final: 0.7546 (t0) REVERT: E 250 GLN cc_start: 0.8197 (tt0) cc_final: 0.7701 (pt0) REVERT: E 294 PHE cc_start: 0.8596 (m-10) cc_final: 0.8314 (m-10) REVERT: E 364 ASN cc_start: 0.6913 (t0) cc_final: 0.6683 (t0) REVERT: E 437 GLN cc_start: 0.8313 (tp40) cc_final: 0.8064 (tp-100) REVERT: F 119 ASP cc_start: 0.7984 (t0) cc_final: 0.7491 (t0) REVERT: F 143 LYS cc_start: 0.8806 (mttt) cc_final: 0.8398 (mtpp) REVERT: F 181 ASP cc_start: 0.7899 (t0) cc_final: 0.7271 (t0) REVERT: F 250 GLN cc_start: 0.7970 (tt0) cc_final: 0.7532 (pt0) REVERT: F 294 PHE cc_start: 0.8615 (m-10) cc_final: 0.8287 (m-80) REVERT: F 437 GLN cc_start: 0.8442 (tp40) cc_final: 0.8199 (tp-100) outliers start: 65 outliers final: 44 residues processed: 307 average time/residue: 0.4246 time to fit residues: 216.7110 Evaluate side-chains 279 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 3.594 ------------------------------------------------------------------------------- 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 263 LEU 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 25 GLU Chi-restraints excluded: chain B residue 102 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 475 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 102 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 469 MET Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 111 optimal weight: 8.9990 chunk 188 optimal weight: 20.0000 chunk 38 optimal weight: 0.0170 chunk 176 optimal weight: 50.0000 chunk 56 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 261 optimal weight: 0.3980 overall best weight: 4.8824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.098886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072166 restraints weight = 60649.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074908 restraints weight = 30701.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076666 restraints weight = 20230.247| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24564 Z= 0.167 Angle : 0.603 8.300 33324 Z= 0.304 Chirality : 0.044 0.152 3612 Planarity : 0.004 0.037 4230 Dihedral : 14.624 160.904 4074 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.72 % Allowed : 11.94 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 2964 helix: 0.19 (0.13), residues: 1494 sheet: -1.87 (0.25), residues: 378 loop : -1.40 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 72 HIS 0.004 0.001 HIS E 258 PHE 0.013 0.002 PHE D 490 TYR 0.020 0.001 TYR C 407 ARG 0.003 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1044) hydrogen bonds : angle 4.51132 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00381 (24564) covalent geometry : angle 0.60349 (33318) *********************** 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 320 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 252 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8687 (p0) cc_final: 0.8243 (p0) REVERT: A 143 LYS cc_start: 0.8861 (mttt) cc_final: 0.8460 (mtpp) REVERT: A 232 TYR cc_start: 0.7896 (m-10) cc_final: 0.7695 (m-10) REVERT: A 233 MET cc_start: 0.7460 (mmt) cc_final: 0.7187 (mmm) REVERT: A 294 PHE cc_start: 0.8752 (m-10) cc_final: 0.8405 (m-80) REVERT: B 25 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (mm-30) REVERT: B 143 LYS cc_start: 0.8882 (mttt) cc_final: 0.8551 (mtpp) REVERT: B 169 MET cc_start: 0.8196 (mmp) cc_final: 0.7954 (mmp) REVERT: B 181 ASP cc_start: 0.7964 (t0) cc_final: 0.7494 (t0) REVERT: B 233 MET cc_start: 0.7259 (tpt) cc_final: 0.7032 (tpt) REVERT: B 250 GLN cc_start: 0.8096 (tt0) cc_final: 0.7101 (pt0) REVERT: B 260 MET cc_start: 0.8489 (tmm) cc_final: 0.7641 (ptm) REVERT: B 294 PHE cc_start: 0.8757 (m-10) cc_final: 0.8417 (m-80) REVERT: B 364 ASN cc_start: 0.7020 (t0) cc_final: 0.6782 (t0) REVERT: B 435 GLU cc_start: 0.8410 (mp0) cc_final: 0.8088 (mp0) REVERT: B 437 GLN cc_start: 0.8384 (tp40) cc_final: 0.8158 (tp-100) REVERT: C 119 ASP cc_start: 0.8025 (t0) cc_final: 0.7543 (t0) REVERT: C 143 LYS cc_start: 0.8812 (mttt) cc_final: 0.8436 (mtpp) REVERT: C 181 ASP cc_start: 0.7907 (t0) cc_final: 0.7422 (t70) REVERT: C 437 GLN cc_start: 0.8479 (tp40) cc_final: 0.8214 (tp-100) REVERT: D 102 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8102 (p0) REVERT: D 143 LYS cc_start: 0.8866 (mttt) cc_final: 0.8465 (mtpp) REVERT: E 25 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: E 143 LYS cc_start: 0.8876 (mttt) cc_final: 0.8549 (mtpp) REVERT: E 169 MET cc_start: 0.8216 (mmp) cc_final: 0.7968 (mmp) REVERT: E 181 ASP cc_start: 0.7976 (t0) cc_final: 0.7692 (t70) REVERT: E 250 GLN cc_start: 0.8189 (tt0) cc_final: 0.7316 (pt0) REVERT: E 294 PHE cc_start: 0.8741 (m-10) cc_final: 0.8410 (m-80) REVERT: E 364 ASN cc_start: 0.7009 (t0) cc_final: 0.6774 (t0) REVERT: E 437 GLN cc_start: 0.8384 (tp40) cc_final: 0.8141 (tp-100) REVERT: F 119 ASP cc_start: 0.8022 (t0) cc_final: 0.7538 (t0) REVERT: F 143 LYS cc_start: 0.8817 (mttt) cc_final: 0.8435 (mtpp) REVERT: F 181 ASP cc_start: 0.7901 (t0) cc_final: 0.7417 (t70) REVERT: F 250 GLN cc_start: 0.7974 (tt0) cc_final: 0.7336 (pt0) REVERT: F 294 PHE cc_start: 0.8670 (m-10) cc_final: 0.8455 (m-10) REVERT: F 437 GLN cc_start: 0.8485 (tp40) cc_final: 0.8250 (tp-100) outliers start: 68 outliers final: 53 residues processed: 299 average time/residue: 0.3202 time to fit residues: 156.4517 Evaluate side-chains 291 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 2.589 ------------------------------------------------------------------------------- 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 191 ASP 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 498 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 191 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 100 SER Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 223 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 95 optimal weight: 0.0670 chunk 40 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073411 restraints weight = 60587.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076163 restraints weight = 30464.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.077979 restraints weight = 19965.530| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24564 Z= 0.123 Angle : 0.573 8.100 33324 Z= 0.287 Chirality : 0.042 0.145 3612 Planarity : 0.004 0.037 4230 Dihedral : 14.084 152.021 4074 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.44 % Allowed : 12.50 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 2964 helix: 0.36 (0.13), residues: 1494 sheet: -1.69 (0.25), residues: 378 loop : -1.23 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 72 HIS 0.004 0.001 HIS C 57 PHE 0.011 0.001 PHE A 490 TYR 0.017 0.001 TYR C 407 ARG 0.004 0.000 ARG E 261 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1044) hydrogen bonds : angle 4.34876 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00282 (24564) covalent geometry : angle 0.57320 (33318) *********************** 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 321 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8684 (p0) cc_final: 0.8212 (p0) REVERT: A 143 LYS cc_start: 0.8845 (mttt) cc_final: 0.8447 (mtpp) REVERT: A 232 TYR cc_start: 0.7848 (m-10) cc_final: 0.6230 (m-10) REVERT: A 233 MET cc_start: 0.7503 (mmt) cc_final: 0.7135 (mmm) REVERT: A 250 GLN cc_start: 0.8377 (pt0) cc_final: 0.8168 (pp30) REVERT: A 294 PHE cc_start: 0.8790 (m-10) cc_final: 0.8449 (m-80) REVERT: B 25 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: B 143 LYS cc_start: 0.8873 (mttt) cc_final: 0.8567 (mtpp) REVERT: B 169 MET cc_start: 0.8230 (mmp) cc_final: 0.7982 (mmp) REVERT: B 181 ASP cc_start: 0.7958 (t0) cc_final: 0.7679 (t70) REVERT: B 260 MET cc_start: 0.8485 (tmm) cc_final: 0.7866 (ptp) REVERT: B 294 PHE cc_start: 0.8779 (m-10) cc_final: 0.8467 (m-80) REVERT: B 364 ASN cc_start: 0.7013 (t0) cc_final: 0.6793 (t0) REVERT: B 435 GLU cc_start: 0.8385 (mp0) cc_final: 0.8104 (mp0) REVERT: B 437 GLN cc_start: 0.8355 (tp40) cc_final: 0.8045 (tp-100) REVERT: C 119 ASP cc_start: 0.7973 (t0) cc_final: 0.7483 (t0) REVERT: C 143 LYS cc_start: 0.8800 (mttt) cc_final: 0.8444 (mtpp) REVERT: C 181 ASP cc_start: 0.7886 (t0) cc_final: 0.7397 (t70) REVERT: C 437 GLN cc_start: 0.8450 (tp40) cc_final: 0.8192 (tp-100) REVERT: D 102 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8068 (p0) REVERT: D 143 LYS cc_start: 0.8850 (mttt) cc_final: 0.8450 (mtpp) REVERT: D 233 MET cc_start: 0.7638 (mmt) cc_final: 0.7312 (mmm) REVERT: D 250 GLN cc_start: 0.8125 (pt0) cc_final: 0.7748 (pt0) REVERT: E 25 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8301 (mm-30) REVERT: E 143 LYS cc_start: 0.8868 (mttt) cc_final: 0.8569 (mtpp) REVERT: E 169 MET cc_start: 0.8224 (mmp) cc_final: 0.7993 (mmp) REVERT: E 181 ASP cc_start: 0.7974 (t0) cc_final: 0.7685 (t70) REVERT: E 294 PHE cc_start: 0.8769 (m-10) cc_final: 0.8466 (m-80) REVERT: E 364 ASN cc_start: 0.6937 (t0) cc_final: 0.6698 (t0) REVERT: E 437 GLN cc_start: 0.8361 (tp40) cc_final: 0.8124 (tp-100) REVERT: F 42 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8081 (tpp80) REVERT: F 119 ASP cc_start: 0.7982 (t0) cc_final: 0.7488 (t0) REVERT: F 143 LYS cc_start: 0.8810 (mttt) cc_final: 0.8447 (mtpp) REVERT: F 181 ASP cc_start: 0.7884 (t0) cc_final: 0.7406 (t70) REVERT: F 250 GLN cc_start: 0.7845 (tt0) cc_final: 0.7344 (pt0) REVERT: F 294 PHE cc_start: 0.8654 (m-10) cc_final: 0.8449 (m-10) REVERT: F 437 GLN cc_start: 0.8459 (tp40) cc_final: 0.8236 (tp-100) outliers start: 61 outliers final: 51 residues processed: 304 average time/residue: 0.3609 time to fit residues: 176.1923 Evaluate side-chains 291 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 2.641 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 498 VAL 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 257 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 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 236 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 498 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 460 SER Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 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 475 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 42 ARG 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 242 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 251 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 95 optimal weight: 0.0010 chunk 21 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 226 optimal weight: 40.0000 chunk 41 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 125 optimal weight: 0.0670 chunk 107 optimal weight: 2.9990 overall best weight: 3.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.099913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073544 restraints weight = 60404.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076291 restraints weight = 30389.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078069 restraints weight = 20007.497| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24564 Z= 0.126 Angle : 0.573 7.818 33324 Z= 0.286 Chirality : 0.043 0.148 3612 Planarity : 0.004 0.039 4230 Dihedral : 13.038 176.361 4074 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.60 % Allowed : 12.50 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2964 helix: 0.39 (0.13), residues: 1518 sheet: -1.70 (0.25), residues: 390 loop : -1.09 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 72 HIS 0.003 0.001 HIS D 298 PHE 0.011 0.001 PHE D 294 TYR 0.019 0.001 TYR A 232 ARG 0.005 0.000 ARG C 462 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 1044) hydrogen bonds : angle 4.30479 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00289 (24564) covalent geometry : angle 0.57276 (33318) *********************** 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 331 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8681 (p0) cc_final: 0.8213 (p0) REVERT: A 143 LYS cc_start: 0.8851 (mttt) cc_final: 0.8441 (mtpp) REVERT: A 294 PHE cc_start: 0.8801 (m-10) cc_final: 0.8460 (m-80) REVERT: B 25 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: B 143 LYS cc_start: 0.8877 (mttt) cc_final: 0.8488 (mtpp) REVERT: B 169 MET cc_start: 0.8235 (mmp) cc_final: 0.8034 (mmp) REVERT: B 181 ASP cc_start: 0.7939 (t0) cc_final: 0.7651 (t70) REVERT: B 260 MET cc_start: 0.8433 (tmm) cc_final: 0.7842 (ptp) REVERT: B 294 PHE cc_start: 0.8777 (m-10) cc_final: 0.8478 (m-80) REVERT: B 435 GLU cc_start: 0.8346 (mp0) cc_final: 0.8106 (mp0) REVERT: B 437 GLN cc_start: 0.8373 (tp40) cc_final: 0.8077 (tp-100) REVERT: C 119 ASP cc_start: 0.7960 (t0) cc_final: 0.7495 (t0) REVERT: C 143 LYS cc_start: 0.8817 (mttt) cc_final: 0.8494 (mtpp) REVERT: C 181 ASP cc_start: 0.7860 (t0) cc_final: 0.7378 (t70) REVERT: C 233 MET cc_start: 0.7383 (tpt) cc_final: 0.7173 (tpt) REVERT: C 330 GLN cc_start: 0.7824 (mt0) cc_final: 0.7558 (mt0) REVERT: C 437 GLN cc_start: 0.8452 (tp40) cc_final: 0.8219 (tp-100) REVERT: D 102 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8054 (p0) REVERT: D 143 LYS cc_start: 0.8865 (mttt) cc_final: 0.8455 (mtpp) REVERT: D 233 MET cc_start: 0.7561 (mmt) cc_final: 0.7091 (mmm) REVERT: D 250 GLN cc_start: 0.8050 (pt0) cc_final: 0.7674 (pt0) REVERT: E 25 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: E 143 LYS cc_start: 0.8874 (mttt) cc_final: 0.8557 (mtpp) REVERT: E 169 MET cc_start: 0.8270 (mmp) cc_final: 0.8017 (mmp) REVERT: E 181 ASP cc_start: 0.7939 (t0) cc_final: 0.7654 (t70) REVERT: E 437 GLN cc_start: 0.8382 (tp40) cc_final: 0.8150 (tp-100) REVERT: F 119 ASP cc_start: 0.7962 (t0) cc_final: 0.7498 (t0) REVERT: F 143 LYS cc_start: 0.8822 (mttt) cc_final: 0.8485 (mtpp) REVERT: F 181 ASP cc_start: 0.7875 (t0) cc_final: 0.7398 (t70) REVERT: F 250 GLN cc_start: 0.7735 (tt0) cc_final: 0.7521 (pt0) REVERT: F 260 MET cc_start: 0.8585 (tmm) cc_final: 0.7621 (ptm) REVERT: F 294 PHE cc_start: 0.8764 (m-10) cc_final: 0.8498 (m-10) REVERT: F 407 TYR cc_start: 0.7686 (p90) cc_final: 0.7455 (p90) REVERT: F 437 GLN cc_start: 0.8463 (tp40) cc_final: 0.8253 (tp-100) outliers start: 65 outliers final: 54 residues processed: 313 average time/residue: 0.3689 time to fit residues: 191.1854 Evaluate side-chains 300 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 2.953 ------------------------------------------------------------------------------- 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 119 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 257 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 100 SER Chi-restraints excluded: chain C residue 236 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 498 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 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 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 127 optimal weight: 7.9990 chunk 291 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071321 restraints weight = 60464.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073988 restraints weight = 30571.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075686 restraints weight = 20169.096| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24564 Z= 0.206 Angle : 0.649 9.722 33324 Z= 0.327 Chirality : 0.045 0.161 3612 Planarity : 0.004 0.037 4230 Dihedral : 12.505 175.234 4074 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.12 % Allowed : 12.54 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 2964 helix: 0.24 (0.13), residues: 1512 sheet: -1.72 (0.25), residues: 390 loop : -1.14 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 72 HIS 0.005 0.001 HIS C 258 PHE 0.020 0.002 PHE E 294 TYR 0.019 0.002 TYR C 407 ARG 0.005 0.001 ARG F 462 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 1044) hydrogen bonds : angle 4.58138 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00467 (24564) covalent geometry : angle 0.64926 (33318) *********************** 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 322 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 244 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8706 (p0) cc_final: 0.8287 (p0) REVERT: A 143 LYS cc_start: 0.8864 (mttt) cc_final: 0.8450 (mtpp) REVERT: A 294 PHE cc_start: 0.8840 (m-10) cc_final: 0.8595 (m-10) REVERT: B 102 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8491 (p0) REVERT: B 143 LYS cc_start: 0.8888 (mttt) cc_final: 0.8539 (mtpp) REVERT: B 169 MET cc_start: 0.8322 (mmp) cc_final: 0.8054 (mmp) REVERT: B 181 ASP cc_start: 0.7902 (t0) cc_final: 0.7602 (t70) REVERT: B 260 MET cc_start: 0.8482 (tmm) cc_final: 0.7860 (ptp) REVERT: B 435 GLU cc_start: 0.8403 (mp0) cc_final: 0.8159 (mp0) REVERT: B 437 GLN cc_start: 0.8411 (tp40) cc_final: 0.7905 (tp-100) REVERT: C 119 ASP cc_start: 0.8101 (t0) cc_final: 0.7613 (t0) REVERT: C 143 LYS cc_start: 0.8830 (mttt) cc_final: 0.8486 (mtpp) REVERT: C 181 ASP cc_start: 0.7895 (t0) cc_final: 0.7405 (t70) REVERT: C 233 MET cc_start: 0.7456 (tpt) cc_final: 0.7249 (tpt) REVERT: C 330 GLN cc_start: 0.7762 (mt0) cc_final: 0.7406 (mt0) REVERT: C 437 GLN cc_start: 0.8470 (tp40) cc_final: 0.8237 (tp-100) REVERT: D 102 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8173 (p0) REVERT: D 143 LYS cc_start: 0.8863 (mttt) cc_final: 0.8451 (mtpp) REVERT: D 233 MET cc_start: 0.7624 (mmt) cc_final: 0.7250 (mmm) REVERT: E 143 LYS cc_start: 0.8891 (mttt) cc_final: 0.8542 (mtpp) REVERT: E 169 MET cc_start: 0.8320 (mmp) cc_final: 0.8076 (mmp) REVERT: E 176 MET cc_start: 0.9164 (mmp) cc_final: 0.8914 (mmp) REVERT: E 181 ASP cc_start: 0.7934 (t0) cc_final: 0.7610 (t70) REVERT: E 233 MET cc_start: 0.7583 (tpp) cc_final: 0.7274 (tpp) REVERT: E 437 GLN cc_start: 0.8403 (tp40) cc_final: 0.8185 (tp-100) REVERT: F 119 ASP cc_start: 0.8109 (t0) cc_final: 0.7620 (t0) REVERT: F 143 LYS cc_start: 0.8836 (mttt) cc_final: 0.8484 (mtpp) REVERT: F 181 ASP cc_start: 0.7881 (t0) cc_final: 0.7398 (t70) REVERT: F 250 GLN cc_start: 0.7853 (tt0) cc_final: 0.7552 (pt0) REVERT: F 260 MET cc_start: 0.8543 (tmm) cc_final: 0.7601 (ptm) REVERT: F 294 PHE cc_start: 0.8803 (m-10) cc_final: 0.8559 (m-10) REVERT: F 437 GLN cc_start: 0.8482 (tp40) cc_final: 0.8193 (tp-100) outliers start: 78 outliers final: 65 residues processed: 301 average time/residue: 0.3377 time to fit residues: 164.3230 Evaluate side-chains 300 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 119 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 498 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 257 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain 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 138 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 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 373 LEU Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 259 optimal weight: 0.9980 chunk 208 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 chunk 104 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 271 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN F 250 GLN ** F 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.098920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.072527 restraints weight = 60263.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.075240 restraints weight = 30330.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076965 restraints weight = 19992.356| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24564 Z= 0.148 Angle : 0.597 8.843 33324 Z= 0.302 Chirality : 0.043 0.149 3612 Planarity : 0.004 0.038 4230 Dihedral : 12.235 176.487 4074 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.48 % Allowed : 13.38 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 2964 helix: 0.41 (0.13), residues: 1476 sheet: -1.66 (0.25), residues: 390 loop : -1.07 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 72 HIS 0.003 0.001 HIS A 298 PHE 0.023 0.002 PHE B 294 TYR 0.016 0.001 TYR C 407 ARG 0.004 0.000 ARG F 462 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 1044) hydrogen bonds : angle 4.44327 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00339 (24564) covalent geometry : angle 0.59743 (33318) ********************** 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 301 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8673 (p0) cc_final: 0.8221 (p0) REVERT: A 143 LYS cc_start: 0.8848 (mttt) cc_final: 0.8450 (mtpp) REVERT: A 233 MET cc_start: 0.7830 (mmt) cc_final: 0.7417 (mmm) REVERT: A 294 PHE cc_start: 0.8829 (m-10) cc_final: 0.8592 (m-10) REVERT: B 143 LYS cc_start: 0.8886 (mttt) cc_final: 0.8572 (mtpp) REVERT: B 169 MET cc_start: 0.8310 (mmp) cc_final: 0.8091 (mmp) REVERT: B 181 ASP cc_start: 0.7901 (t0) cc_final: 0.7577 (t70) REVERT: B 233 MET cc_start: 0.7322 (tpt) cc_final: 0.6794 (tpp) REVERT: B 260 MET cc_start: 0.8489 (tmm) cc_final: 0.7897 (ptp) REVERT: B 435 GLU cc_start: 0.8356 (mp0) cc_final: 0.8124 (mp0) REVERT: B 437 GLN cc_start: 0.8391 (tp40) cc_final: 0.8140 (tp-100) REVERT: C 119 ASP cc_start: 0.8028 (t0) cc_final: 0.7547 (t0) REVERT: C 143 LYS cc_start: 0.8836 (mttt) cc_final: 0.8482 (mtpp) REVERT: C 181 ASP cc_start: 0.7865 (t0) cc_final: 0.7371 (t70) REVERT: C 330 GLN cc_start: 0.7840 (mt0) cc_final: 0.7512 (mt0) REVERT: C 437 GLN cc_start: 0.8457 (tp40) cc_final: 0.8237 (tp-100) REVERT: D 102 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8098 (p0) REVERT: D 143 LYS cc_start: 0.8856 (mttt) cc_final: 0.8454 (mtpp) REVERT: D 233 MET cc_start: 0.7587 (mmt) cc_final: 0.7206 (mmm) REVERT: D 250 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: D 366 MET cc_start: 0.7782 (ttt) cc_final: 0.7535 (ttm) REVERT: E 143 LYS cc_start: 0.8882 (mttt) cc_final: 0.8569 (mtpp) REVERT: E 169 MET cc_start: 0.8314 (mmp) cc_final: 0.8090 (mmp) REVERT: E 181 ASP cc_start: 0.7918 (t0) cc_final: 0.7591 (t70) REVERT: E 437 GLN cc_start: 0.8411 (tp40) cc_final: 0.8202 (tp-100) REVERT: F 119 ASP cc_start: 0.8035 (t0) cc_final: 0.7549 (t0) REVERT: F 143 LYS cc_start: 0.8841 (mttt) cc_final: 0.8484 (mtpp) REVERT: F 181 ASP cc_start: 0.7873 (t0) cc_final: 0.7394 (t70) REVERT: F 250 GLN cc_start: 0.7808 (tt0) cc_final: 0.6938 (pt0) REVERT: F 260 MET cc_start: 0.8515 (tmm) cc_final: 0.7526 (ptm) REVERT: F 294 PHE cc_start: 0.8819 (m-10) cc_final: 0.8579 (m-10) REVERT: F 330 GLN cc_start: 0.7982 (mm110) cc_final: 0.7589 (mt0) REVERT: F 407 TYR cc_start: 0.7759 (p90) cc_final: 0.7511 (p90) REVERT: F 437 GLN cc_start: 0.8461 (tp40) cc_final: 0.8187 (tp-100) outliers start: 62 outliers final: 55 residues processed: 289 average time/residue: 0.3154 time to fit residues: 151.6337 Evaluate side-chains 289 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 2.594 ------------------------------------------------------------------------------- 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 119 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 498 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 257 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 138 ASP Chi-restraints excluded: chain C residue 236 LEU 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 498 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 250 GLN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 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 45 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 243 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** 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 = 0.3650 r_free = 0.3650 target = 0.099364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073060 restraints weight = 60095.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075770 restraints weight = 30298.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077488 restraints weight = 20022.819| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- 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 = 0.82 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: 0.8202 moved from start: 0.4810 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= 0.136 Angle : 0.586 7.584 33324 Z= 0.297 Chirality : 0.043 0.225 3612 Planarity : 0.004 0.038 4230 Dihedral : 11.970 177.604 4074 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.44 % Allowed : 13.38 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 2964 helix: 0.51 (0.13), residues: 1476 sheet: -1.60 (0.25), residues: 390 loop : -1.03 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 72 HIS 0.003 0.001 HIS E 57 PHE 0.027 0.002 PHE B 294 TYR 0.015 0.001 TYR C 407 ARG 0.004 0.000 ARG F 462 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 1044) hydrogen bonds : angle 4.38775 ( 2934) SS BOND : angle 0.00000 ( 6) covalent geometry : bond 0.00314 (24564) covalent geometry : angle 0.58612 (33318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8652.41 seconds wall clock time: 154 minutes 13.72 seconds (9253.72 seconds total)