Starting phenix.real_space_refine on Sun Feb 8 06:07:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m6k_63664/02_2026/9m6k_63664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m6k_63664/02_2026/9m6k_63664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m6k_63664/02_2026/9m6k_63664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m6k_63664/02_2026/9m6k_63664.map" model { file = "/net/cci-nas-00/data/ceres_data/9m6k_63664/02_2026/9m6k_63664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m6k_63664/02_2026/9m6k_63664.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 25836 2.51 5 N 6768 2.21 5 O 8196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41004 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "B" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "C" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "D" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "E" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "F" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "G" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "H" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "I" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "J" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "K" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "L" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3417 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 15, 'TRANS': 410} Time building chain proxies: 8.60, per 1000 atoms: 0.21 Number of scatterers: 41004 At special positions: 0 Unit cell: (181.2, 181.2, 130.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 8196 8.00 N 6768 7.00 C 25836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.28 Conformation dependent library (CDL) restraints added in 1.6 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9816 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 48 sheets defined 49.1% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 20 through 47 Proline residue: A 36 - end of helix removed outlier: 3.703A pdb=" N GLY A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.605A pdb=" N PHE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.829A pdb=" N GLU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 225 through 246 removed outlier: 3.558A pdb=" N ASP A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 removed outlier: 4.014A pdb=" N LYS A 265 " --> pdb=" O MET A 262 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 266 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 312 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.673A pdb=" N LYS A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 360 removed outlier: 4.124A pdb=" N LYS A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 removed outlier: 4.133A pdb=" N TRP A 374 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG A 375 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 377 " --> pdb=" O TRP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 400 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.529A pdb=" N VAL A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.562A pdb=" N GLU A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 47 Proline residue: B 36 - end of helix removed outlier: 3.634A pdb=" N GLY B 47 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.571A pdb=" N PHE B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.662A pdb=" N GLU B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 225 through 246 removed outlier: 3.527A pdb=" N ILE B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 266 removed outlier: 4.042A pdb=" N LYS B 265 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 266 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 312 Processing helix chain 'B' and resid 327 through 333 removed outlier: 4.017A pdb=" N ALA B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 360 removed outlier: 4.135A pdb=" N LYS B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 377 removed outlier: 3.509A pdb=" N SER B 371 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN B 372 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TRP B 374 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG B 375 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 400 Processing helix chain 'B' and resid 404 through 412 removed outlier: 3.527A pdb=" N VAL B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 Processing helix chain 'C' and resid 20 through 47 Proline residue: C 36 - end of helix removed outlier: 3.692A pdb=" N GLY C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.638A pdb=" N PHE C 52 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 108 through 123 removed outlier: 3.895A pdb=" N GLU C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 225 through 246 removed outlier: 3.538A pdb=" N ILE C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 removed outlier: 4.025A pdb=" N LYS C 265 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 266 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 312 removed outlier: 3.508A pdb=" N ALA C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.702A pdb=" N LYS C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 360 removed outlier: 3.617A pdb=" N ARG C 346 " --> pdb=" O ALA C 342 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 377 removed outlier: 3.501A pdb=" N SER C 371 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN C 372 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP C 374 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG C 375 " --> pdb=" O ASN C 372 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 377 " --> pdb=" O TRP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 Processing helix chain 'C' and resid 404 through 412 removed outlier: 3.590A pdb=" N VAL C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 412 " --> pdb=" O THR C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 429 Processing helix chain 'D' and resid 20 through 47 Proline residue: D 36 - end of helix removed outlier: 3.660A pdb=" N GLY D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 removed outlier: 3.609A pdb=" N PHE D 52 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 93 through 108 Processing helix chain 'D' and resid 108 through 124 removed outlier: 3.813A pdb=" N GLU D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 225 through 246 removed outlier: 3.501A pdb=" N ILE D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 removed outlier: 4.017A pdb=" N LYS D 265 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 266 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 312 removed outlier: 3.501A pdb=" N ALA D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 334 removed outlier: 3.675A pdb=" N LYS D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 360 removed outlier: 3.597A pdb=" N ARG D 346 " --> pdb=" O ALA D 342 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET D 360 " --> pdb=" O TYR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 377 removed outlier: 4.589A pdb=" N ASN D 372 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP D 374 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG D 375 " --> pdb=" O ASN D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 400 Processing helix chain 'D' and resid 404 through 412 removed outlier: 3.547A pdb=" N VAL D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 412 " --> pdb=" O THR D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 429 Processing helix chain 'E' and resid 20 through 47 Proline residue: E 36 - end of helix removed outlier: 3.633A pdb=" N GLY E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 54 removed outlier: 3.571A pdb=" N PHE E 52 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 83 Processing helix chain 'E' and resid 93 through 108 Processing helix chain 'E' and resid 108 through 124 removed outlier: 3.651A pdb=" N GLU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 225 through 246 removed outlier: 3.528A pdb=" N ILE E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N PHE E 246 " --> pdb=" O ASP E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 266 removed outlier: 4.174A pdb=" N LYS E 265 " --> pdb=" O MET E 262 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE E 266 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 312 Processing helix chain 'E' and resid 327 through 333 removed outlier: 4.017A pdb=" N ALA E 331 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 360 removed outlier: 4.137A pdb=" N LYS E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 350 " --> pdb=" O ARG E 346 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 377 removed outlier: 3.508A pdb=" N SER E 371 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN E 372 " --> pdb=" O ASN E 369 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TRP E 374 " --> pdb=" O SER E 371 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG E 375 " --> pdb=" O ASN E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 400 Processing helix chain 'E' and resid 404 through 412 removed outlier: 3.526A pdb=" N VAL E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU E 412 " --> pdb=" O THR E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 429 Processing helix chain 'F' and resid 20 through 47 Proline residue: F 36 - end of helix removed outlier: 3.680A pdb=" N GLY F 47 " --> pdb=" O LYS F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.636A pdb=" N PHE F 52 " --> pdb=" O ALA F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 Processing helix chain 'F' and resid 93 through 108 Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.898A pdb=" N GLU F 112 " --> pdb=" O ASP F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 225 through 246 removed outlier: 3.537A pdb=" N ILE F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR F 245 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE F 246 " --> pdb=" O ASP F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 266 removed outlier: 4.053A pdb=" N LYS F 265 " --> pdb=" O MET F 262 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE F 266 " --> pdb=" O ILE F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 312 removed outlier: 3.513A pdb=" N ALA F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 334 removed outlier: 3.702A pdb=" N LYS F 333 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 360 removed outlier: 4.174A pdb=" N LYS F 347 " --> pdb=" O ALA F 343 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET F 360 " --> pdb=" O TYR F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 377 removed outlier: 3.502A pdb=" N SER F 371 " --> pdb=" O ALA F 368 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN F 372 " --> pdb=" O ASN F 369 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP F 374 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG F 375 " --> pdb=" O ASN F 372 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 377 " --> pdb=" O TRP F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 400 Processing helix chain 'F' and resid 404 through 412 removed outlier: 3.570A pdb=" N VAL F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 412 " --> pdb=" O THR F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 429 Processing helix chain 'G' and resid 20 through 47 Proline residue: G 36 - end of helix removed outlier: 3.660A pdb=" N GLY G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 removed outlier: 3.608A pdb=" N PHE G 52 " --> pdb=" O ALA G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 83 Processing helix chain 'G' and resid 93 through 108 Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.804A pdb=" N GLU G 112 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 225 through 246 removed outlier: 3.502A pdb=" N ILE G 229 " --> pdb=" O VAL G 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE G 246 " --> pdb=" O ASP G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 266 removed outlier: 4.014A pdb=" N LYS G 265 " --> pdb=" O MET G 262 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE G 266 " --> pdb=" O ILE G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 312 Processing helix chain 'G' and resid 328 through 334 removed outlier: 3.677A pdb=" N LYS G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 360 removed outlier: 4.125A pdb=" N LYS G 347 " --> pdb=" O ALA G 343 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 350 " --> pdb=" O ARG G 346 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET G 360 " --> pdb=" O TYR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 377 removed outlier: 4.568A pdb=" N ASN G 372 " --> pdb=" O ASN G 369 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP G 374 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG G 375 " --> pdb=" O ASN G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 400 Processing helix chain 'G' and resid 404 through 412 removed outlier: 3.535A pdb=" N VAL G 411 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU G 412 " --> pdb=" O THR G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 429 Processing helix chain 'H' and resid 20 through 47 Proline residue: H 36 - end of helix removed outlier: 3.678A pdb=" N GLY H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 54 removed outlier: 3.585A pdb=" N PHE H 52 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 83 Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 108 through 123 removed outlier: 3.650A pdb=" N GLU H 112 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 225 through 246 removed outlier: 3.530A pdb=" N ILE H 229 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE H 246 " --> pdb=" O ASP H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 removed outlier: 4.036A pdb=" N LYS H 265 " --> pdb=" O MET H 262 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE H 266 " --> pdb=" O ILE H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 312 Processing helix chain 'H' and resid 327 through 333 removed outlier: 4.016A pdb=" N ALA H 331 " --> pdb=" O GLY H 327 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 360 removed outlier: 4.137A pdb=" N LYS H 347 " --> pdb=" O ALA H 343 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA H 350 " --> pdb=" O ARG H 346 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET H 360 " --> pdb=" O TYR H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 377 removed outlier: 3.508A pdb=" N SER H 371 " --> pdb=" O ALA H 368 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN H 372 " --> pdb=" O ASN H 369 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP H 374 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG H 375 " --> pdb=" O ASN H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 400 Processing helix chain 'H' and resid 404 through 412 removed outlier: 3.543A pdb=" N VAL H 411 " --> pdb=" O THR H 407 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU H 412 " --> pdb=" O THR H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 429 Processing helix chain 'I' and resid 20 through 47 Proline residue: I 36 - end of helix removed outlier: 3.679A pdb=" N GLY I 47 " --> pdb=" O LYS I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.636A pdb=" N PHE I 52 " --> pdb=" O ALA I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 83 Processing helix chain 'I' and resid 93 through 108 Processing helix chain 'I' and resid 108 through 123 removed outlier: 3.897A pdb=" N GLU I 112 " --> pdb=" O ASP I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 224 No H-bonds generated for 'chain 'I' and resid 222 through 224' Processing helix chain 'I' and resid 225 through 246 removed outlier: 3.536A pdb=" N ILE I 229 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP I 244 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR I 245 " --> pdb=" O ASN I 241 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE I 246 " --> pdb=" O ASP I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 266 removed outlier: 4.054A pdb=" N LYS I 265 " --> pdb=" O MET I 262 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE I 266 " --> pdb=" O ILE I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 312 removed outlier: 3.515A pdb=" N ALA I 312 " --> pdb=" O ILE I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 334 removed outlier: 3.703A pdb=" N LYS I 333 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU I 334 " --> pdb=" O LEU I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 360 removed outlier: 4.152A pdb=" N LYS I 347 " --> pdb=" O ALA I 343 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET I 360 " --> pdb=" O TYR I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 377 removed outlier: 4.563A pdb=" N ASN I 372 " --> pdb=" O ASN I 369 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP I 374 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG I 375 " --> pdb=" O ASN I 372 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE I 377 " --> pdb=" O TRP I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 400 Processing helix chain 'I' and resid 404 through 412 removed outlier: 3.585A pdb=" N VAL I 411 " --> pdb=" O THR I 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU I 412 " --> pdb=" O THR I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 429 Processing helix chain 'J' and resid 20 through 47 Proline residue: J 36 - end of helix removed outlier: 3.660A pdb=" N GLY J 47 " --> pdb=" O LYS J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 removed outlier: 3.613A pdb=" N PHE J 52 " --> pdb=" O ALA J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 83 Processing helix chain 'J' and resid 93 through 108 Processing helix chain 'J' and resid 108 through 123 removed outlier: 3.815A pdb=" N GLU J 112 " --> pdb=" O ASP J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 225 through 246 removed outlier: 3.512A pdb=" N ILE J 229 " --> pdb=" O VAL J 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP J 244 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR J 245 " --> pdb=" O ASN J 241 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE J 246 " --> pdb=" O ASP J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 266 removed outlier: 3.985A pdb=" N LYS J 265 " --> pdb=" O MET J 262 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE J 266 " --> pdb=" O ILE J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 312 Processing helix chain 'J' and resid 328 through 334 removed outlier: 3.684A pdb=" N LYS J 333 " --> pdb=" O ALA J 329 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU J 334 " --> pdb=" O LEU J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 360 removed outlier: 4.131A pdb=" N LYS J 347 " --> pdb=" O ALA J 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA J 350 " --> pdb=" O ARG J 346 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET J 360 " --> pdb=" O TYR J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 377 removed outlier: 3.502A pdb=" N SER J 371 " --> pdb=" O ALA J 368 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN J 372 " --> pdb=" O ASN J 369 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP J 374 " --> pdb=" O SER J 371 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG J 375 " --> pdb=" O ASN J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 400 Processing helix chain 'J' and resid 404 through 412 removed outlier: 3.551A pdb=" N VAL J 411 " --> pdb=" O THR J 407 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU J 412 " --> pdb=" O THR J 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 429 Processing helix chain 'K' and resid 20 through 47 Proline residue: K 36 - end of helix removed outlier: 3.633A pdb=" N GLY K 47 " --> pdb=" O LYS K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 54 removed outlier: 3.573A pdb=" N PHE K 52 " --> pdb=" O ALA K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 83 Processing helix chain 'K' and resid 93 through 108 Processing helix chain 'K' and resid 108 through 123 removed outlier: 3.653A pdb=" N GLU K 112 " --> pdb=" O ASP K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 225 through 246 removed outlier: 3.529A pdb=" N ILE K 229 " --> pdb=" O VAL K 225 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP K 244 " --> pdb=" O THR K 240 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR K 245 " --> pdb=" O ASN K 241 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE K 246 " --> pdb=" O ASP K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 266 removed outlier: 4.174A pdb=" N LYS K 265 " --> pdb=" O MET K 262 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE K 266 " --> pdb=" O ILE K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 312 Processing helix chain 'K' and resid 327 through 333 removed outlier: 4.017A pdb=" N ALA K 331 " --> pdb=" O GLY K 327 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS K 333 " --> pdb=" O ALA K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 360 removed outlier: 4.164A pdb=" N LYS K 347 " --> pdb=" O ALA K 343 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET K 360 " --> pdb=" O TYR K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 377 removed outlier: 3.505A pdb=" N SER K 371 " --> pdb=" O ALA K 368 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN K 372 " --> pdb=" O ASN K 369 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TRP K 374 " --> pdb=" O SER K 371 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG K 375 " --> pdb=" O ASN K 372 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE K 377 " --> pdb=" O TRP K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 400 Processing helix chain 'K' and resid 404 through 412 removed outlier: 3.534A pdb=" N VAL K 411 " --> pdb=" O THR K 407 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU K 412 " --> pdb=" O THR K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 429 Processing helix chain 'L' and resid 20 through 47 Proline residue: L 36 - end of helix removed outlier: 3.686A pdb=" N GLY L 47 " --> pdb=" O LYS L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 54 removed outlier: 3.638A pdb=" N PHE L 52 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 83 Processing helix chain 'L' and resid 93 through 108 Processing helix chain 'L' and resid 108 through 123 removed outlier: 3.906A pdb=" N GLU L 112 " --> pdb=" O ASP L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 224 No H-bonds generated for 'chain 'L' and resid 222 through 224' Processing helix chain 'L' and resid 225 through 246 removed outlier: 3.538A pdb=" N ILE L 229 " --> pdb=" O VAL L 225 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP L 244 " --> pdb=" O THR L 240 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR L 245 " --> pdb=" O ASN L 241 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE L 246 " --> pdb=" O ASP L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 266 removed outlier: 4.047A pdb=" N LYS L 265 " --> pdb=" O MET L 262 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE L 266 " --> pdb=" O ILE L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 312 removed outlier: 3.514A pdb=" N ALA L 312 " --> pdb=" O ILE L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 334 removed outlier: 3.704A pdb=" N LYS L 333 " --> pdb=" O ALA L 329 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU L 334 " --> pdb=" O LEU L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 360 removed outlier: 4.153A pdb=" N LYS L 347 " --> pdb=" O ALA L 343 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET L 360 " --> pdb=" O TYR L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 377 removed outlier: 4.559A pdb=" N ASN L 372 " --> pdb=" O ASN L 369 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP L 374 " --> pdb=" O SER L 371 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG L 375 " --> pdb=" O ASN L 372 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE L 377 " --> pdb=" O TRP L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 400 Processing helix chain 'L' and resid 404 through 412 removed outlier: 3.571A pdb=" N VAL L 411 " --> pdb=" O THR L 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU L 412 " --> pdb=" O THR L 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 417 through 429 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 4.680A pdb=" N PHE A 11 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP A 153 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP A 184 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 199 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 186 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.588A pdb=" N ASN A 90 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 378 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 143 removed outlier: 3.536A pdb=" N PHE A 127 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 289 removed outlier: 8.472A pdb=" N ILE B 272 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 251 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL B 274 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 253 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 13 removed outlier: 4.652A pdb=" N PHE B 11 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP B 153 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP B 184 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU B 199 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR B 186 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.525A pdb=" N ASN B 90 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 378 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 143 Processing sheet with id=AA9, first strand: chain 'B' and resid 284 through 289 removed outlier: 8.512A pdb=" N ILE C 272 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 251 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL C 274 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 253 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.499A pdb=" N PHE C 11 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 183 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP C 184 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU C 199 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR C 186 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.542A pdb=" N ASN C 90 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 378 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 143 removed outlier: 3.576A pdb=" N PHE C 127 " --> pdb=" O ASN C 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 284 through 289 removed outlier: 8.490A pdb=" N ILE D 272 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU C 251 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL D 274 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 253 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 13 removed outlier: 4.685A pdb=" N PHE D 11 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASP D 153 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 183 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP D 184 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU D 199 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR D 186 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 88 through 90 removed outlier: 3.602A pdb=" N ASN D 90 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 378 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 143 removed outlier: 3.525A pdb=" N PHE D 127 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 284 through 289 removed outlier: 8.464A pdb=" N ILE E 272 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU D 251 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL E 274 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 253 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 13 removed outlier: 4.649A pdb=" N PHE E 11 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASP E 153 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP E 184 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU E 199 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR E 186 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 88 through 90 removed outlier: 3.526A pdb=" N ASN E 90 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 378 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 138 through 143 Processing sheet with id=AC3, first strand: chain 'E' and resid 284 through 289 removed outlier: 8.508A pdb=" N ILE F 272 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU E 251 " --> pdb=" O ILE F 272 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL F 274 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL E 253 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.483A pdb=" N PHE F 11 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL F 183 " --> pdb=" O THR F 180 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP F 184 " --> pdb=" O GLU F 199 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU F 199 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR F 186 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 88 through 90 removed outlier: 3.530A pdb=" N ASN F 90 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 378 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 138 through 143 removed outlier: 3.576A pdb=" N PHE F 127 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 284 through 289 removed outlier: 8.494A pdb=" N ILE G 272 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU F 251 " --> pdb=" O ILE G 272 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL G 274 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL F 253 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 13 removed outlier: 4.686A pdb=" N PHE G 11 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP G 153 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP G 184 " --> pdb=" O GLU G 199 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU G 199 " --> pdb=" O ASP G 184 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR G 186 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 88 through 90 removed outlier: 3.592A pdb=" N ASN G 90 " --> pdb=" O GLU G 378 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 378 " --> pdb=" O ASN G 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 138 through 143 Processing sheet with id=AD2, first strand: chain 'G' and resid 284 through 289 removed outlier: 8.470A pdb=" N ILE H 272 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU G 251 " --> pdb=" O ILE H 272 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL H 274 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL G 253 " --> pdb=" O VAL H 274 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.449A pdb=" N PHE H 11 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP H 184 " --> pdb=" O GLU H 199 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU H 199 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR H 186 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 88 through 90 removed outlier: 3.535A pdb=" N ASN H 90 " --> pdb=" O GLU H 378 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 138 through 143 Processing sheet with id=AD6, first strand: chain 'H' and resid 284 through 289 removed outlier: 8.513A pdb=" N ILE I 272 " --> pdb=" O SER H 249 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU H 251 " --> pdb=" O ILE I 272 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL I 274 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL H 253 " --> pdb=" O VAL I 274 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.471A pdb=" N PHE I 11 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL I 183 " --> pdb=" O THR I 180 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP I 184 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU I 199 " --> pdb=" O ASP I 184 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR I 186 " --> pdb=" O GLY I 197 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 88 through 90 removed outlier: 3.556A pdb=" N ASN I 90 " --> pdb=" O GLU I 378 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU I 378 " --> pdb=" O ASN I 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 138 through 143 removed outlier: 3.578A pdb=" N PHE I 127 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 284 through 289 removed outlier: 8.491A pdb=" N ILE J 272 " --> pdb=" O SER I 249 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU I 251 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL J 274 " --> pdb=" O LEU I 251 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL I 253 " --> pdb=" O VAL J 274 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 13 removed outlier: 4.686A pdb=" N PHE J 11 " --> pdb=" O ILE J 150 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP J 153 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP J 184 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU J 199 " --> pdb=" O ASP J 184 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR J 186 " --> pdb=" O GLY J 197 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 88 through 90 removed outlier: 3.605A pdb=" N ASN J 90 " --> pdb=" O GLU J 378 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU J 378 " --> pdb=" O ASN J 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 138 through 143 removed outlier: 3.515A pdb=" N PHE J 127 " --> pdb=" O ASN J 143 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 284 through 289 removed outlier: 8.470A pdb=" N ILE K 272 " --> pdb=" O SER J 249 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU J 251 " --> pdb=" O ILE K 272 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL K 274 " --> pdb=" O LEU J 251 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL J 253 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.395A pdb=" N PHE K 11 " --> pdb=" O TYR K 152 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL K 183 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP K 184 " --> pdb=" O GLU K 199 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU K 199 " --> pdb=" O ASP K 184 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR K 186 " --> pdb=" O GLY K 197 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 88 through 90 removed outlier: 3.533A pdb=" N ASN K 90 " --> pdb=" O GLU K 378 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU K 378 " --> pdb=" O ASN K 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 138 through 143 Processing sheet with id=AE9, first strand: chain 'K' and resid 284 through 289 removed outlier: 8.496A pdb=" N ILE L 272 " --> pdb=" O SER K 249 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU K 251 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL L 274 " --> pdb=" O LEU K 251 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL K 253 " --> pdb=" O VAL L 274 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.455A pdb=" N PHE L 11 " --> pdb=" O TYR L 152 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL L 183 " --> pdb=" O THR L 180 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP L 184 " --> pdb=" O GLU L 199 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU L 199 " --> pdb=" O ASP L 184 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR L 186 " --> pdb=" O GLY L 197 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 88 through 90 removed outlier: 3.554A pdb=" N ASN L 90 " --> pdb=" O GLU L 378 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU L 378 " --> pdb=" O ASN L 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 138 through 143 removed outlier: 3.575A pdb=" N PHE L 127 " --> pdb=" O ASN L 143 " (cutoff:3.500A) 1975 hydrogen bonds defined for protein. 5571 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: 8.59 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13793 1.34 - 1.46: 7579 1.46 - 1.58: 20016 1.58 - 1.69: 0 1.69 - 1.81: 384 Bond restraints: 41772 Sorted by residual: bond pdb=" CA GLN K 35 " pdb=" C GLN K 35 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.29e-02 6.01e+03 1.09e+00 bond pdb=" CA GLN L 35 " pdb=" C GLN L 35 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.29e-02 6.01e+03 1.09e+00 bond pdb=" CA GLN H 35 " pdb=" C GLN H 35 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.29e-02 6.01e+03 1.03e+00 bond pdb=" CA GLN F 35 " pdb=" C GLN F 35 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.29e-02 6.01e+03 1.01e+00 bond pdb=" CA GLN I 35 " pdb=" C GLN I 35 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.29e-02 6.01e+03 9.98e-01 ... (remaining 41767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 53214 0.88 - 1.77: 2564 1.77 - 2.65: 448 2.65 - 3.53: 217 3.53 - 4.42: 41 Bond angle restraints: 56484 Sorted by residual: angle pdb=" N PRO C 59 " pdb=" CA PRO C 59 " pdb=" C PRO C 59 " ideal model delta sigma weight residual 113.53 116.47 -2.94 1.39e+00 5.18e-01 4.46e+00 angle pdb=" C GLU L 58 " pdb=" CA GLU L 58 " pdb=" CB GLU L 58 " ideal model delta sigma weight residual 109.51 113.40 -3.89 1.85e+00 2.92e-01 4.41e+00 angle pdb=" N ILE B 317 " pdb=" CA ILE B 317 " pdb=" C ILE B 317 " ideal model delta sigma weight residual 110.42 112.43 -2.01 9.60e-01 1.09e+00 4.39e+00 angle pdb=" C GLU C 58 " pdb=" CA GLU C 58 " pdb=" CB GLU C 58 " ideal model delta sigma weight residual 109.51 113.38 -3.87 1.85e+00 2.92e-01 4.38e+00 angle pdb=" N PRO I 59 " pdb=" CA PRO I 59 " pdb=" C PRO I 59 " ideal model delta sigma weight residual 113.53 116.43 -2.90 1.39e+00 5.18e-01 4.36e+00 ... (remaining 56479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 23109 17.96 - 35.93: 2070 35.93 - 53.89: 270 53.89 - 71.85: 47 71.85 - 89.82: 16 Dihedral angle restraints: 25512 sinusoidal: 10392 harmonic: 15120 Sorted by residual: dihedral pdb=" CA GLU C 58 " pdb=" C GLU C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta harmonic sigma weight residual 180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLU F 58 " pdb=" C GLU F 58 " pdb=" N PRO F 59 " pdb=" CA PRO F 59 " ideal model delta harmonic sigma weight residual 180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLU I 58 " pdb=" C GLU I 58 " pdb=" N PRO I 59 " pdb=" CA PRO I 59 " ideal model delta harmonic sigma weight residual 180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 25509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4602 0.033 - 0.067: 1162 0.067 - 0.100: 306 0.100 - 0.134: 189 0.134 - 0.167: 5 Chirality restraints: 6264 Sorted by residual: chirality pdb=" CA PRO C 59 " pdb=" N PRO C 59 " pdb=" C PRO C 59 " pdb=" CB PRO C 59 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA PRO F 59 " pdb=" N PRO F 59 " pdb=" C PRO F 59 " pdb=" CB PRO F 59 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA PRO I 59 " pdb=" N PRO I 59 " pdb=" C PRO I 59 " pdb=" CB PRO I 59 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 6261 not shown) Planarity restraints: 7452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 374 " 0.012 2.00e-02 2.50e+03 1.23e-02 3.78e+00 pdb=" CG TRP F 374 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP F 374 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP F 374 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 374 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 374 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 374 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 374 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 374 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP F 374 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 374 " 0.012 2.00e-02 2.50e+03 1.23e-02 3.77e+00 pdb=" CG TRP I 374 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP I 374 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP I 374 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP I 374 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 374 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 374 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 374 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 374 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP I 374 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 374 " 0.012 2.00e-02 2.50e+03 1.17e-02 3.40e+00 pdb=" CG TRP L 374 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP L 374 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP L 374 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 374 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 374 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 374 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 374 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 374 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 374 " 0.000 2.00e-02 2.50e+03 ... (remaining 7449 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7479 2.77 - 3.30: 37412 3.30 - 3.84: 60614 3.84 - 4.37: 67409 4.37 - 4.90: 124712 Nonbonded interactions: 297626 Sorted by model distance: nonbonded pdb=" NZ LYS J 234 " pdb=" OD2 ASP K 244 " model vdw 2.240 3.120 nonbonded pdb=" NZ LYS G 234 " pdb=" OD2 ASP H 244 " model vdw 2.249 3.120 nonbonded pdb=" NZ LYS D 234 " pdb=" OD2 ASP E 244 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS F 239 " pdb=" OE2 GLU F 298 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS I 239 " pdb=" OE2 GLU I 298 " model vdw 2.258 3.120 ... (remaining 297621 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.320 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.002 0.025 41772 Z= 0.117 Angle : 0.471 4.416 56484 Z= 0.275 Chirality : 0.037 0.167 6264 Planarity : 0.004 0.044 7452 Dihedral : 13.293 89.816 15696 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.12), residues: 5088 helix: 2.97 (0.11), residues: 2088 sheet: 1.91 (0.18), residues: 804 loop : -1.27 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 375 TYR 0.007 0.001 TYR K 356 PHE 0.011 0.001 PHE B 162 TRP 0.033 0.004 TRP I 374 HIS 0.003 0.000 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00218 (41772) covalent geometry : angle 0.47062 (56484) hydrogen bonds : bond 0.20088 ( 1975) hydrogen bonds : angle 5.44052 ( 5571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 821 time to evaluate : 1.392 Fit side-chains REVERT: A 372 ASN cc_start: 0.8853 (m-40) cc_final: 0.8627 (t0) REVERT: B 184 ASP cc_start: 0.7782 (m-30) cc_final: 0.7474 (t0) REVERT: D 372 ASN cc_start: 0.8768 (m-40) cc_final: 0.8466 (t0) REVERT: D 426 HIS cc_start: 0.8479 (t70) cc_final: 0.8209 (t70) REVERT: E 184 ASP cc_start: 0.7832 (m-30) cc_final: 0.7448 (t0) REVERT: G 372 ASN cc_start: 0.8778 (m-40) cc_final: 0.8547 (t0) REVERT: H 33 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8582 (ttmm) REVERT: H 184 ASP cc_start: 0.7832 (m-30) cc_final: 0.7475 (t0) REVERT: I 205 ASN cc_start: 0.8328 (p0) cc_final: 0.7964 (p0) REVERT: I 206 ASP cc_start: 0.8528 (t0) cc_final: 0.8175 (m-30) REVERT: J 372 ASN cc_start: 0.8760 (m-40) cc_final: 0.8526 (t0) REVERT: J 375 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8317 (mtt-85) REVERT: K 184 ASP cc_start: 0.7836 (m-30) cc_final: 0.7506 (t0) outliers start: 0 outliers final: 0 residues processed: 821 average time/residue: 0.2316 time to fit residues: 314.1402 Evaluate side-chains 661 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 661 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 494 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 142 HIS B 64 ASN E 64 ASN E 102 ASN ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS G 64 ASN H 64 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS J 142 HIS K 64 ASN L 142 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.086113 restraints weight = 65006.711| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.83 r_work: 0.2865 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 41772 Z= 0.311 Angle : 0.636 7.364 56484 Z= 0.346 Chirality : 0.046 0.153 6264 Planarity : 0.005 0.061 7452 Dihedral : 4.310 18.024 5532 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 7.89 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 5088 helix: 2.55 (0.11), residues: 2124 sheet: 1.24 (0.18), residues: 864 loop : -1.42 (0.11), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 424 TYR 0.021 0.002 TYR C 179 PHE 0.021 0.002 PHE L 287 TRP 0.015 0.002 TRP C 374 HIS 0.005 0.001 HIS E 91 Details of bonding type rmsd covalent geometry : bond 0.00781 (41772) covalent geometry : angle 0.63645 (56484) hydrogen bonds : bond 0.08343 ( 1975) hydrogen bonds : angle 4.51359 ( 5571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 670 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 ASN cc_start: 0.9149 (m-40) cc_final: 0.8703 (t0) REVERT: D 426 HIS cc_start: 0.8771 (t70) cc_final: 0.8541 (t70) REVERT: G 372 ASN cc_start: 0.9075 (m-40) cc_final: 0.8647 (t0) REVERT: H 33 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8638 (ttmm) REVERT: J 372 ASN cc_start: 0.9035 (m-40) cc_final: 0.8628 (t0) REVERT: J 375 ARG cc_start: 0.8897 (mtt-85) cc_final: 0.8284 (mtt-85) outliers start: 89 outliers final: 66 residues processed: 726 average time/residue: 0.2158 time to fit residues: 256.9697 Evaluate side-chains 681 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 615 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 418 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 418 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 418 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 221 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 457 optimal weight: 7.9990 chunk 361 optimal weight: 8.9990 chunk 486 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 473 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 393 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN B 93 ASN C 93 ASN D 93 ASN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN F 93 ASN G 93 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN J 93 ASN ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.089671 restraints weight = 63860.932| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.82 r_work: 0.2916 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41772 Z= 0.146 Angle : 0.494 7.277 56484 Z= 0.270 Chirality : 0.040 0.144 6264 Planarity : 0.004 0.037 7452 Dihedral : 4.137 17.632 5532 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.58 % Allowed : 10.11 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.12), residues: 5088 helix: 2.77 (0.11), residues: 2124 sheet: 1.19 (0.18), residues: 864 loop : -1.28 (0.11), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 375 TYR 0.012 0.001 TYR K 179 PHE 0.013 0.001 PHE L 287 TRP 0.019 0.002 TRP F 374 HIS 0.003 0.001 HIS L 307 Details of bonding type rmsd covalent geometry : bond 0.00341 (41772) covalent geometry : angle 0.49353 (56484) hydrogen bonds : bond 0.05997 ( 1975) hydrogen bonds : angle 4.00610 ( 5571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 660 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ASN cc_start: 0.9119 (m-40) cc_final: 0.8641 (t0) REVERT: B 171 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7536 (mp0) REVERT: B 184 ASP cc_start: 0.7966 (m-30) cc_final: 0.7486 (t0) REVERT: E 171 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7533 (mp0) REVERT: G 372 ASN cc_start: 0.9031 (m-40) cc_final: 0.8647 (t0) REVERT: G 374 TRP cc_start: 0.8799 (p-90) cc_final: 0.8593 (p90) REVERT: H 33 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8667 (ttmm) REVERT: H 184 ASP cc_start: 0.7939 (m-30) cc_final: 0.7429 (t0) REVERT: J 372 ASN cc_start: 0.9087 (m-40) cc_final: 0.8618 (t0) REVERT: J 375 ARG cc_start: 0.8882 (mtt-85) cc_final: 0.8362 (mtt-85) REVERT: K 171 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7534 (mp0) outliers start: 72 outliers final: 55 residues processed: 708 average time/residue: 0.2164 time to fit residues: 254.7926 Evaluate side-chains 678 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 623 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 448 optimal weight: 0.9990 chunk 292 optimal weight: 10.0000 chunk 408 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 chunk 494 optimal weight: 2.9990 chunk 490 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 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 = 0.3459 r_free = 0.3459 target = 0.118073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090119 restraints weight = 63586.517| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.81 r_work: 0.2924 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41772 Z= 0.139 Angle : 0.475 7.342 56484 Z= 0.260 Chirality : 0.040 0.135 6264 Planarity : 0.003 0.035 7452 Dihedral : 4.008 18.248 5532 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 11.25 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 5088 helix: 2.83 (0.11), residues: 2124 sheet: 1.21 (0.18), residues: 864 loop : -1.23 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 375 TYR 0.012 0.001 TYR K 179 PHE 0.011 0.001 PHE L 162 TRP 0.020 0.002 TRP K 374 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00326 (41772) covalent geometry : angle 0.47519 (56484) hydrogen bonds : bond 0.05567 ( 1975) hydrogen bonds : angle 3.84637 ( 5571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 642 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6775 (tm-30) REVERT: B 171 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7542 (mp0) REVERT: E 171 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7539 (mp0) REVERT: E 238 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8007 (mm-30) REVERT: G 372 ASN cc_start: 0.9032 (m-40) cc_final: 0.8628 (t0) REVERT: G 374 TRP cc_start: 0.8790 (p-90) cc_final: 0.8576 (p90) REVERT: J 372 ASN cc_start: 0.9084 (m-40) cc_final: 0.8605 (t0) REVERT: J 375 ARG cc_start: 0.8918 (mtt-85) cc_final: 0.8421 (mtt-85) REVERT: K 171 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7540 (mp0) REVERT: K 238 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8011 (mm-30) outliers start: 79 outliers final: 69 residues processed: 688 average time/residue: 0.2201 time to fit residues: 252.6611 Evaluate side-chains 692 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 623 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 265 LYS Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 8.9990 chunk 464 optimal weight: 8.9990 chunk 371 optimal weight: 9.9990 chunk 270 optimal weight: 0.0370 chunk 224 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 440 optimal weight: 7.9990 chunk 154 optimal weight: 0.1980 chunk 443 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 overall best weight: 2.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS C 142 HIS ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.089338 restraints weight = 63469.104| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.81 r_work: 0.2915 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 41772 Z= 0.157 Angle : 0.482 6.799 56484 Z= 0.263 Chirality : 0.040 0.136 6264 Planarity : 0.003 0.034 7452 Dihedral : 3.968 18.700 5532 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.93 % Allowed : 12.43 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.12), residues: 5088 helix: 2.83 (0.11), residues: 2124 sheet: 1.15 (0.18), residues: 864 loop : -1.21 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 375 TYR 0.013 0.001 TYR K 179 PHE 0.013 0.001 PHE A 287 TRP 0.022 0.002 TRP C 374 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00377 (41772) covalent geometry : angle 0.48152 (56484) hydrogen bonds : bond 0.05751 ( 1975) hydrogen bonds : angle 3.80155 ( 5571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 646 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.9339 (tp) cc_final: 0.9055 (tt) REVERT: A 198 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6720 (tm-30) REVERT: B 184 ASP cc_start: 0.7937 (m-30) cc_final: 0.7530 (t0) REVERT: E 161 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8704 (tt) REVERT: E 238 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7961 (mm-30) REVERT: G 372 ASN cc_start: 0.9045 (m-40) cc_final: 0.8602 (t0) REVERT: G 374 TRP cc_start: 0.8788 (p-90) cc_final: 0.8550 (p90) REVERT: H 184 ASP cc_start: 0.7882 (m-30) cc_final: 0.7447 (t0) REVERT: K 171 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7541 (mp0) REVERT: K 238 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7975 (mm-30) outliers start: 88 outliers final: 76 residues processed: 704 average time/residue: 0.2166 time to fit residues: 253.9390 Evaluate side-chains 702 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 625 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 265 LYS Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 265 LYS Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 415 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 399 optimal weight: 3.9990 chunk 462 optimal weight: 5.9990 chunk 467 optimal weight: 0.0670 chunk 254 optimal weight: 10.0000 chunk 374 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.089389 restraints weight = 63956.423| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.74 r_work: 0.2932 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 41772 Z= 0.162 Angle : 0.488 6.814 56484 Z= 0.267 Chirality : 0.040 0.135 6264 Planarity : 0.003 0.041 7452 Dihedral : 3.961 18.253 5532 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.00 % Allowed : 12.81 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.12), residues: 5088 helix: 2.81 (0.11), residues: 2124 sheet: 1.13 (0.18), residues: 864 loop : -1.19 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 375 TYR 0.013 0.001 TYR K 179 PHE 0.013 0.001 PHE D 287 TRP 0.036 0.003 TRP J 374 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00393 (41772) covalent geometry : angle 0.48759 (56484) hydrogen bonds : bond 0.05772 ( 1975) hydrogen bonds : angle 3.79010 ( 5571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 643 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.9357 (tp) cc_final: 0.9069 (tt) REVERT: A 198 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6742 (tm-30) REVERT: B 161 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8716 (tt) REVERT: B 184 ASP cc_start: 0.7910 (m-30) cc_final: 0.7551 (t0) REVERT: E 161 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8715 (tt) REVERT: E 238 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8034 (mm-30) REVERT: G 372 ASN cc_start: 0.8972 (m-40) cc_final: 0.8572 (t0) REVERT: G 374 TRP cc_start: 0.8801 (p-90) cc_final: 0.8565 (p90) REVERT: H 161 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8666 (tt) REVERT: H 184 ASP cc_start: 0.7891 (m-30) cc_final: 0.7482 (t0) REVERT: K 161 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8717 (tt) REVERT: K 238 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8024 (mm-30) outliers start: 91 outliers final: 70 residues processed: 703 average time/residue: 0.2202 time to fit residues: 257.4806 Evaluate side-chains 694 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 620 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 265 LYS Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 466 optimal weight: 0.9980 chunk 426 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 501 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 370 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: C 205 ASN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** 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 = 0.3410 r_free = 0.3410 target = 0.114561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.086800 restraints weight = 64193.159| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.71 r_work: 0.2871 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 41772 Z= 0.235 Angle : 0.561 9.081 56484 Z= 0.305 Chirality : 0.043 0.141 6264 Planarity : 0.004 0.041 7452 Dihedral : 4.142 18.333 5532 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.91 % Allowed : 13.44 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.12), residues: 5088 helix: 2.97 (0.11), residues: 2052 sheet: 0.92 (0.18), residues: 864 loop : -1.16 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 375 TYR 0.017 0.002 TYR K 179 PHE 0.019 0.002 PHE D 287 TRP 0.068 0.003 TRP J 374 HIS 0.003 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00583 (41772) covalent geometry : angle 0.56148 (56484) hydrogen bonds : bond 0.06973 ( 1975) hydrogen bonds : angle 3.98777 ( 5571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 602 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.9357 (tp) cc_final: 0.9076 (tt) REVERT: A 198 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 161 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8675 (tt) REVERT: B 184 ASP cc_start: 0.7994 (m-30) cc_final: 0.7559 (t0) REVERT: B 330 LEU cc_start: 0.9325 (mm) cc_final: 0.9058 (mm) REVERT: E 184 ASP cc_start: 0.8006 (m-30) cc_final: 0.7492 (t0) REVERT: E 330 LEU cc_start: 0.9327 (mm) cc_final: 0.9057 (mm) REVERT: G 372 ASN cc_start: 0.8996 (m-40) cc_final: 0.8562 (t0) REVERT: G 374 TRP cc_start: 0.8854 (p-90) cc_final: 0.8521 (p90) REVERT: H 161 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8708 (tt) REVERT: H 184 ASP cc_start: 0.7979 (m-30) cc_final: 0.7494 (t0) REVERT: H 330 LEU cc_start: 0.9326 (mm) cc_final: 0.9054 (mm) REVERT: K 161 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8698 (tt) REVERT: K 238 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8247 (mm-30) outliers start: 87 outliers final: 71 residues processed: 657 average time/residue: 0.2225 time to fit residues: 242.0028 Evaluate side-chains 675 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 601 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 265 LYS Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 265 LYS Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 174 optimal weight: 3.9990 chunk 349 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 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 = 0.3421 r_free = 0.3421 target = 0.115351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.087612 restraints weight = 63766.324| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.71 r_work: 0.2889 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 41772 Z= 0.202 Angle : 0.536 7.067 56484 Z= 0.292 Chirality : 0.042 0.139 6264 Planarity : 0.004 0.033 7452 Dihedral : 4.119 18.225 5532 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 14.06 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.12), residues: 5088 helix: 2.97 (0.11), residues: 2052 sheet: 0.85 (0.18), residues: 864 loop : -1.13 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 375 TYR 0.014 0.001 TYR K 179 PHE 0.015 0.002 PHE J 287 TRP 0.081 0.004 TRP J 374 HIS 0.002 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00497 (41772) covalent geometry : angle 0.53575 (56484) hydrogen bonds : bond 0.06472 ( 1975) hydrogen bonds : angle 3.90961 ( 5571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 609 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.9323 (tp) cc_final: 0.9045 (tt) REVERT: A 198 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6726 (tm-30) REVERT: B 161 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8692 (tt) REVERT: B 184 ASP cc_start: 0.7916 (m-30) cc_final: 0.7620 (t0) REVERT: B 330 LEU cc_start: 0.9311 (mm) cc_final: 0.9059 (mm) REVERT: E 161 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8718 (tt) REVERT: E 330 LEU cc_start: 0.9311 (mm) cc_final: 0.9054 (mm) REVERT: G 372 ASN cc_start: 0.8980 (m-40) cc_final: 0.8527 (t0) REVERT: H 161 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8732 (tt) REVERT: H 184 ASP cc_start: 0.7967 (m-30) cc_final: 0.7492 (t0) REVERT: H 330 LEU cc_start: 0.9309 (mm) cc_final: 0.9053 (mm) REVERT: K 161 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8759 (tt) REVERT: K 238 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8240 (mm-30) outliers start: 85 outliers final: 71 residues processed: 664 average time/residue: 0.2344 time to fit residues: 258.7226 Evaluate side-chains 680 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 605 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 265 LYS Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 265 LYS Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 486 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 474 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 0.0770 chunk 339 optimal weight: 5.9990 chunk 496 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 ASN J 354 GLN ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089585 restraints weight = 63714.230| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.73 r_work: 0.2923 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41772 Z= 0.139 Angle : 0.497 9.029 56484 Z= 0.270 Chirality : 0.040 0.134 6264 Planarity : 0.003 0.040 7452 Dihedral : 3.986 18.372 5532 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.62 % Allowed : 14.63 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.12), residues: 5088 helix: 3.09 (0.11), residues: 2052 sheet: 0.95 (0.18), residues: 864 loop : -1.02 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 375 TYR 0.015 0.001 TYR J 356 PHE 0.013 0.001 PHE A 212 TRP 0.098 0.004 TRP J 374 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00324 (41772) covalent geometry : angle 0.49698 (56484) hydrogen bonds : bond 0.05435 ( 1975) hydrogen bonds : angle 3.73859 ( 5571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 619 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.9348 (tp) cc_final: 0.9073 (tt) REVERT: A 198 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6694 (tm-30) REVERT: B 161 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8716 (tt) REVERT: B 184 ASP cc_start: 0.7890 (m-30) cc_final: 0.7605 (t0) REVERT: B 330 LEU cc_start: 0.9292 (mm) cc_final: 0.9059 (mm) REVERT: E 161 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8708 (tt) REVERT: E 184 ASP cc_start: 0.7925 (m-30) cc_final: 0.7488 (t0) REVERT: E 330 LEU cc_start: 0.9290 (mm) cc_final: 0.9060 (mm) REVERT: G 372 ASN cc_start: 0.8983 (m-40) cc_final: 0.8629 (t0) REVERT: G 374 TRP cc_start: 0.8827 (p-90) cc_final: 0.8534 (p90) REVERT: H 161 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8716 (tt) REVERT: H 184 ASP cc_start: 0.7881 (m-30) cc_final: 0.7525 (t0) REVERT: H 330 LEU cc_start: 0.9288 (mm) cc_final: 0.9056 (mm) REVERT: J 373 GLU cc_start: 0.8597 (tp30) cc_final: 0.7736 (tp30) REVERT: K 161 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8717 (tt) REVERT: K 238 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8097 (mm-30) outliers start: 74 outliers final: 65 residues processed: 668 average time/residue: 0.2327 time to fit residues: 257.6073 Evaluate side-chains 681 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 612 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 265 LYS Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 265 LYS Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 154 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 311 optimal weight: 0.5980 chunk 362 optimal weight: 0.0570 chunk 249 optimal weight: 8.9990 chunk 450 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 307 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN F 205 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 ASN ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088072 restraints weight = 63663.767| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.71 r_work: 0.2892 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 41772 Z= 0.191 Angle : 0.530 6.903 56484 Z= 0.288 Chirality : 0.041 0.137 6264 Planarity : 0.004 0.037 7452 Dihedral : 4.051 18.338 5532 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.58 % Allowed : 14.74 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.12), residues: 5088 helix: 3.04 (0.11), residues: 2052 sheet: 0.86 (0.18), residues: 864 loop : -1.06 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 375 TYR 0.014 0.001 TYR K 179 PHE 0.015 0.002 PHE D 287 TRP 0.096 0.004 TRP J 374 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00469 (41772) covalent geometry : angle 0.53038 (56484) hydrogen bonds : bond 0.06177 ( 1975) hydrogen bonds : angle 3.82242 ( 5571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 610 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.9349 (tp) cc_final: 0.9077 (tt) REVERT: A 198 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6712 (tm-30) REVERT: B 161 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8697 (tt) REVERT: B 184 ASP cc_start: 0.8007 (m-30) cc_final: 0.7746 (t0) REVERT: B 330 LEU cc_start: 0.9294 (mm) cc_final: 0.9051 (mm) REVERT: C 184 ASP cc_start: 0.8150 (m-30) cc_final: 0.7697 (t0) REVERT: E 161 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8664 (tt) REVERT: E 184 ASP cc_start: 0.7922 (m-30) cc_final: 0.7512 (t0) REVERT: E 330 LEU cc_start: 0.9311 (mm) cc_final: 0.9067 (mm) REVERT: F 184 ASP cc_start: 0.8126 (m-30) cc_final: 0.7694 (t0) REVERT: G 372 ASN cc_start: 0.8987 (m-40) cc_final: 0.8627 (t0) REVERT: G 374 TRP cc_start: 0.8849 (p-90) cc_final: 0.8522 (p90) REVERT: H 161 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8721 (tt) REVERT: H 184 ASP cc_start: 0.7907 (m-30) cc_final: 0.7526 (t0) REVERT: H 330 LEU cc_start: 0.9309 (mm) cc_final: 0.9066 (mm) REVERT: J 188 ILE cc_start: 0.9388 (tp) cc_final: 0.9125 (tt) REVERT: J 373 GLU cc_start: 0.8625 (tp30) cc_final: 0.7814 (tp30) REVERT: J 374 TRP cc_start: 0.7627 (p-90) cc_final: 0.7416 (p-90) REVERT: J 375 ARG cc_start: 0.8886 (mtt-85) cc_final: 0.8667 (mtt-85) REVERT: K 161 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8735 (tt) REVERT: K 238 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8120 (mm-30) REVERT: L 184 ASP cc_start: 0.8135 (m-30) cc_final: 0.7696 (t0) outliers start: 72 outliers final: 68 residues processed: 658 average time/residue: 0.2416 time to fit residues: 262.0110 Evaluate side-chains 679 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 607 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 265 LYS Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 319 ASP Chi-restraints excluded: chain H residue 328 VAL Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 292 ASP Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 265 LYS Chi-restraints excluded: chain J residue 292 ASP Chi-restraints excluded: chain J residue 319 ASP Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 188 ILE Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain K residue 292 ASP Chi-restraints excluded: chain K residue 319 ASP Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 58 GLU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain L residue 265 LYS Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 319 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 451 optimal weight: 0.5980 chunk 116 optimal weight: 8.9990 chunk 495 optimal weight: 3.9990 chunk 423 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 449 optimal weight: 1.9990 chunk 487 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 444 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 ASN ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090038 restraints weight = 63455.679| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.80 r_work: 0.2929 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41772 Z= 0.128 Angle : 0.492 7.139 56484 Z= 0.267 Chirality : 0.040 0.134 6264 Planarity : 0.003 0.035 7452 Dihedral : 3.920 18.599 5532 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.51 % Allowed : 15.18 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.12), residues: 5088 helix: 3.16 (0.11), residues: 2052 sheet: 1.01 (0.18), residues: 864 loop : -0.95 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 375 TYR 0.010 0.001 TYR K 179 PHE 0.012 0.001 PHE J 322 TRP 0.082 0.004 TRP J 374 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00296 (41772) covalent geometry : angle 0.49235 (56484) hydrogen bonds : bond 0.05044 ( 1975) hydrogen bonds : angle 3.65223 ( 5571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7934.38 seconds wall clock time: 137 minutes 10.17 seconds (8230.17 seconds total)