Starting phenix.real_space_refine on Fri Aug 7 14:56:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ec_75103/08_2026/10ec_75103.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ec_75103/08_2026/10ec_75103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10ec_75103/08_2026/10ec_75103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ec_75103/08_2026/10ec_75103.map" model { file = "/net/cci-nas-00/data/ceres_data/10ec_75103/08_2026/10ec_75103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ec_75103/08_2026/10ec_75103.cif" } resolution = 4.46 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= 0.003 sd= 0.039 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: 3 Type Number sf(0) Gaussians C 10944 2.51 5 N 5472 2.21 5 O 5472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21888 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 1824 Classifications: {'peptide': 456} Incomplete info: {'backbone_only': 428} Link IDs: {'PTRANS': 19, 'TRANS': 436} Chain breaks: 2 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1740 Unresolved non-hydrogen angles: 2550 Unresolved non-hydrogen dihedrals: 1070 Unresolved non-hydrogen chiralities: 557 Planarities with less than four sites: {'ASN:plan1': 23, 'ASP:plan': 34, 'GLN:plan1': 23, 'HIS:plan': 9, 'TYR:plan': 10, 'ARG:plan': 24, 'GLU:plan': 23, 'TRP:plan': 7, 'PHE:plan': 12} Unresolved non-hydrogen planarities: 820 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 2.67, per 1000 atoms: 0.12 Number of scatterers: 21888 At special positions: 0 Unit cell: (175.275, 175.275, 122.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 5472 8.00 N 5472 7.00 C 10944 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: 2.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 36 sheets defined 47.6% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA A 13 " --> pdb=" O HIS A 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Proline residue: A 17 - end of helix removed outlier: 3.507A pdb=" N GLY A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 35 Processing helix chain 'A' and resid 36 through 39 Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 Processing helix chain 'A' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.518A pdb=" N LYS A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 448 through 460 Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Proline residue: B 17 - end of helix removed outlier: 3.507A pdb=" N GLY B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 35 Processing helix chain 'B' and resid 36 through 39 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 345 through 361 removed outlier: 3.519A pdb=" N LYS B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR B 384 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 444 Processing helix chain 'B' and resid 448 through 460 Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA C 13 " --> pdb=" O HIS C 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Proline residue: C 17 - end of helix removed outlier: 3.507A pdb=" N GLY C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE C 98 " --> pdb=" O MET C 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 345 through 361 removed outlier: 3.519A pdb=" N LYS C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR C 384 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE C 388 " --> pdb=" O THR C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 444 Processing helix chain 'C' and resid 448 through 460 Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA D 13 " --> pdb=" O HIS D 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Proline residue: D 17 - end of helix removed outlier: 3.507A pdb=" N GLY D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 Processing helix chain 'D' and resid 36 through 39 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG D 72 " --> pdb=" O ASN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 Processing helix chain 'D' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN D 280 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP D 289 " --> pdb=" O ASN D 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 345 through 361 removed outlier: 3.518A pdb=" N LYS D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR D 384 " --> pdb=" O TYR D 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE D 388 " --> pdb=" O THR D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 448 through 460 Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA E 13 " --> pdb=" O HIS E 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) Proline residue: E 17 - end of helix removed outlier: 3.507A pdb=" N GLY E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 Processing helix chain 'E' and resid 36 through 39 Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG E 72 " --> pdb=" O ASN E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE E 98 " --> pdb=" O MET E 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 123 Processing helix chain 'E' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN E 280 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU E 287 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP E 289 " --> pdb=" O ASN E 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 315 Processing helix chain 'E' and resid 316 through 319 Processing helix chain 'E' and resid 345 through 361 removed outlier: 3.519A pdb=" N LYS E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR E 384 " --> pdb=" O TYR E 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER E 387 " --> pdb=" O GLN E 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE E 388 " --> pdb=" O THR E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 448 through 460 Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP E 473 " --> pdb=" O GLU E 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA F 13 " --> pdb=" O HIS F 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Proline residue: F 17 - end of helix removed outlier: 3.507A pdb=" N GLY F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 35 Processing helix chain 'F' and resid 36 through 39 Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 Processing helix chain 'F' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU F 287 " --> pdb=" O HIS F 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP F 289 " --> pdb=" O ASN F 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 315 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 345 through 361 removed outlier: 3.519A pdb=" N LYS F 360 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR F 384 " --> pdb=" O TYR F 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER F 387 " --> pdb=" O GLN F 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE F 388 " --> pdb=" O THR F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 448 through 460 Processing helix chain 'F' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP F 473 " --> pdb=" O GLU F 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA G 13 " --> pdb=" O HIS G 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG G 14 " --> pdb=" O PRO G 10 " (cutoff:3.500A) Proline residue: G 17 - end of helix removed outlier: 3.507A pdb=" N GLY G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 35 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 50 through 63 Processing helix chain 'G' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 93 No H-bonds generated for 'chain 'G' and resid 91 through 93' Processing helix chain 'G' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE G 98 " --> pdb=" O MET G 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 123 Processing helix chain 'G' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN G 280 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 287 " --> pdb=" O HIS G 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP G 289 " --> pdb=" O ASN G 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 315 Processing helix chain 'G' and resid 316 through 319 Processing helix chain 'G' and resid 345 through 361 removed outlier: 3.518A pdb=" N LYS G 360 " --> pdb=" O LEU G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR G 384 " --> pdb=" O TYR G 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP G 385 " --> pdb=" O ASP G 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER G 387 " --> pdb=" O GLN G 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE G 388 " --> pdb=" O THR G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 444 Processing helix chain 'G' and resid 448 through 460 Processing helix chain 'G' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP G 473 " --> pdb=" O GLU G 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA H 13 " --> pdb=" O HIS H 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG H 14 " --> pdb=" O PRO H 10 " (cutoff:3.500A) Proline residue: H 17 - end of helix removed outlier: 3.507A pdb=" N GLY H 28 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 35 Processing helix chain 'H' and resid 36 through 39 Processing helix chain 'H' and resid 50 through 63 Processing helix chain 'H' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE H 98 " --> pdb=" O MET H 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 Processing helix chain 'H' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN H 280 " --> pdb=" O ILE H 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU H 287 " --> pdb=" O HIS H 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA H 288 " --> pdb=" O TYR H 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP H 289 " --> pdb=" O ASN H 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA H 294 " --> pdb=" O VAL H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 315 Processing helix chain 'H' and resid 316 through 319 Processing helix chain 'H' and resid 345 through 361 removed outlier: 3.519A pdb=" N LYS H 360 " --> pdb=" O LEU H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR H 384 " --> pdb=" O TYR H 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP H 385 " --> pdb=" O ASP H 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER H 387 " --> pdb=" O GLN H 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE H 388 " --> pdb=" O THR H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 444 Processing helix chain 'H' and resid 448 through 460 Processing helix chain 'H' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP H 473 " --> pdb=" O GLU H 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA I 13 " --> pdb=" O HIS I 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG I 14 " --> pdb=" O PRO I 10 " (cutoff:3.500A) Proline residue: I 17 - end of helix removed outlier: 3.507A pdb=" N GLY I 28 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 35 Processing helix chain 'I' and resid 36 through 39 Processing helix chain 'I' and resid 50 through 63 Processing helix chain 'I' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG I 72 " --> pdb=" O ASN I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'I' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE I 98 " --> pdb=" O MET I 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 123 Processing helix chain 'I' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN I 280 " --> pdb=" O ILE I 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU I 287 " --> pdb=" O HIS I 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA I 288 " --> pdb=" O TYR I 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP I 289 " --> pdb=" O ASN I 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA I 294 " --> pdb=" O VAL I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 315 Processing helix chain 'I' and resid 316 through 319 Processing helix chain 'I' and resid 345 through 361 removed outlier: 3.519A pdb=" N LYS I 360 " --> pdb=" O LEU I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR I 384 " --> pdb=" O TYR I 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP I 385 " --> pdb=" O ASP I 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER I 387 " --> pdb=" O GLN I 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE I 388 " --> pdb=" O THR I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 444 Processing helix chain 'I' and resid 448 through 460 Processing helix chain 'I' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP I 473 " --> pdb=" O GLU I 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA J 13 " --> pdb=" O HIS J 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG J 14 " --> pdb=" O PRO J 10 " (cutoff:3.500A) Proline residue: J 17 - end of helix removed outlier: 3.507A pdb=" N GLY J 28 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 35 Processing helix chain 'J' and resid 36 through 39 Processing helix chain 'J' and resid 50 through 63 Processing helix chain 'J' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG J 72 " --> pdb=" O ASN J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 93 No H-bonds generated for 'chain 'J' and resid 91 through 93' Processing helix chain 'J' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE J 98 " --> pdb=" O MET J 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 123 Processing helix chain 'J' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN J 280 " --> pdb=" O ILE J 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU J 287 " --> pdb=" O HIS J 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA J 288 " --> pdb=" O TYR J 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP J 289 " --> pdb=" O ASN J 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA J 294 " --> pdb=" O VAL J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 315 Processing helix chain 'J' and resid 316 through 319 Processing helix chain 'J' and resid 345 through 361 removed outlier: 3.518A pdb=" N LYS J 360 " --> pdb=" O LEU J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR J 384 " --> pdb=" O TYR J 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP J 385 " --> pdb=" O ASP J 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER J 387 " --> pdb=" O GLN J 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE J 388 " --> pdb=" O THR J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 444 Processing helix chain 'J' and resid 448 through 460 Processing helix chain 'J' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP J 473 " --> pdb=" O GLU J 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA K 13 " --> pdb=" O HIS K 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG K 14 " --> pdb=" O PRO K 10 " (cutoff:3.500A) Proline residue: K 17 - end of helix removed outlier: 3.507A pdb=" N GLY K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 35 Processing helix chain 'K' and resid 36 through 39 Processing helix chain 'K' and resid 50 through 63 Processing helix chain 'K' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG K 72 " --> pdb=" O ASN K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 93 No H-bonds generated for 'chain 'K' and resid 91 through 93' Processing helix chain 'K' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE K 98 " --> pdb=" O MET K 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP K 99 " --> pdb=" O ALA K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 123 Processing helix chain 'K' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN K 280 " --> pdb=" O ILE K 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU K 287 " --> pdb=" O HIS K 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA K 288 " --> pdb=" O TYR K 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA K 294 " --> pdb=" O VAL K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 315 Processing helix chain 'K' and resid 316 through 319 Processing helix chain 'K' and resid 345 through 361 removed outlier: 3.519A pdb=" N LYS K 360 " --> pdb=" O LEU K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR K 384 " --> pdb=" O TYR K 380 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP K 385 " --> pdb=" O ASP K 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER K 387 " --> pdb=" O GLN K 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE K 388 " --> pdb=" O THR K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 444 Processing helix chain 'K' and resid 448 through 460 Processing helix chain 'K' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP K 473 " --> pdb=" O GLU K 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 28 removed outlier: 3.802A pdb=" N ALA L 13 " --> pdb=" O HIS L 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG L 14 " --> pdb=" O PRO L 10 " (cutoff:3.500A) Proline residue: L 17 - end of helix removed outlier: 3.507A pdb=" N GLY L 28 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 35 Processing helix chain 'L' and resid 36 through 39 Processing helix chain 'L' and resid 50 through 63 Processing helix chain 'L' and resid 68 through 82 removed outlier: 4.099A pdb=" N ARG L 72 " --> pdb=" O ASN L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 93 No H-bonds generated for 'chain 'L' and resid 91 through 93' Processing helix chain 'L' and resid 94 through 101 removed outlier: 3.549A pdb=" N ILE L 98 " --> pdb=" O MET L 94 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 123 Processing helix chain 'L' and resid 273 through 296 removed outlier: 3.534A pdb=" N ASN L 280 " --> pdb=" O ILE L 276 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU L 287 " --> pdb=" O HIS L 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP L 289 " --> pdb=" O ASN L 285 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA L 294 " --> pdb=" O VAL L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 315 Processing helix chain 'L' and resid 316 through 319 Processing helix chain 'L' and resid 345 through 361 removed outlier: 3.519A pdb=" N LYS L 360 " --> pdb=" O LEU L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 411 removed outlier: 4.511A pdb=" N THR L 384 " --> pdb=" O TYR L 380 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP L 385 " --> pdb=" O ASP L 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER L 387 " --> pdb=" O GLN L 383 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE L 388 " --> pdb=" O THR L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 444 Processing helix chain 'L' and resid 448 through 460 Processing helix chain 'L' and resid 469 through 478 removed outlier: 3.831A pdb=" N ASP L 473 " --> pdb=" O GLU L 469 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY A 126 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 127 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 166 through 172 removed outlier: 7.416A pdb=" N ILE A 166 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 181 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN A 168 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 179 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG A 170 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 179 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 201 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 215 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG A 217 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP A 239 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE A 219 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A 237 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 301 through 305 removed outlier: 3.689A pdb=" N VAL A 303 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY B 126 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 127 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 166 through 172 removed outlier: 7.417A pdb=" N ILE B 166 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 181 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN B 168 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 179 " --> pdb=" O ASN B 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG B 170 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 179 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 201 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 215 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG B 217 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP B 239 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 219 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG B 237 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 301 through 305 removed outlier: 3.689A pdb=" N VAL B 303 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY C 126 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE C 127 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 166 through 172 removed outlier: 7.417A pdb=" N ILE C 166 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 181 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN C 168 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE C 179 " --> pdb=" O ASN C 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG C 170 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 179 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 201 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 215 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG C 217 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP C 239 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE C 219 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG C 237 " --> pdb=" O PHE C 219 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 301 through 305 removed outlier: 3.690A pdb=" N VAL C 303 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY D 126 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 127 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'D' and resid 166 through 172 removed outlier: 7.416A pdb=" N ILE D 166 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU D 181 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN D 168 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE D 179 " --> pdb=" O ASN D 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG D 170 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 179 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR D 201 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 215 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG D 217 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP D 239 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE D 219 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG D 237 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'D' and resid 301 through 305 removed outlier: 3.689A pdb=" N VAL D 303 " --> pdb=" O LYS D 337 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'E' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY E 126 " --> pdb=" O TYR E 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 127 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'E' and resid 166 through 172 removed outlier: 7.417A pdb=" N ILE E 166 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU E 181 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN E 168 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 179 " --> pdb=" O ASN E 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG E 170 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 179 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR E 201 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA E 215 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG E 217 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP E 239 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE E 219 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG E 237 " --> pdb=" O PHE E 219 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'E' and resid 301 through 305 removed outlier: 3.689A pdb=" N VAL E 303 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'F' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY F 126 " --> pdb=" O TYR F 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE F 127 " --> pdb=" O CYS F 257 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 166 through 172 removed outlier: 7.417A pdb=" N ILE F 166 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU F 181 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN F 168 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE F 179 " --> pdb=" O ASN F 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG F 170 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 179 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR F 201 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA F 215 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG F 217 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP F 239 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE F 219 " --> pdb=" O ARG F 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG F 237 " --> pdb=" O PHE F 219 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'F' and resid 301 through 305 removed outlier: 3.690A pdb=" N VAL F 303 " --> pdb=" O LYS F 337 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'G' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY G 126 " --> pdb=" O TYR G 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE G 127 " --> pdb=" O CYS G 257 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'G' and resid 166 through 172 removed outlier: 7.416A pdb=" N ILE G 166 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU G 181 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN G 168 " --> pdb=" O ILE G 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE G 179 " --> pdb=" O ASN G 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG G 170 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G 179 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR G 201 " --> pdb=" O TYR G 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA G 215 " --> pdb=" O VAL G 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG G 217 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP G 239 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE G 219 " --> pdb=" O ARG G 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG G 237 " --> pdb=" O PHE G 219 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'G' and resid 301 through 305 removed outlier: 3.689A pdb=" N VAL G 303 " --> pdb=" O LYS G 337 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'H' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY H 126 " --> pdb=" O TYR H 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE H 127 " --> pdb=" O CYS H 257 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'H' and resid 166 through 172 removed outlier: 7.417A pdb=" N ILE H 166 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU H 181 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN H 168 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE H 179 " --> pdb=" O ASN H 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG H 170 " --> pdb=" O THR H 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE H 179 " --> pdb=" O LEU H 206 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR H 201 " --> pdb=" O TYR H 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA H 215 " --> pdb=" O VAL H 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG H 217 " --> pdb=" O ASP H 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP H 239 " --> pdb=" O ARG H 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE H 219 " --> pdb=" O ARG H 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG H 237 " --> pdb=" O PHE H 219 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'H' and resid 301 through 305 removed outlier: 3.689A pdb=" N VAL H 303 " --> pdb=" O LYS H 337 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'I' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY I 126 " --> pdb=" O TYR I 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE I 127 " --> pdb=" O CYS I 257 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'I' and resid 166 through 172 removed outlier: 7.417A pdb=" N ILE I 166 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU I 181 " --> pdb=" O ILE I 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN I 168 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE I 179 " --> pdb=" O ASN I 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG I 170 " --> pdb=" O THR I 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE I 179 " --> pdb=" O LEU I 206 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR I 201 " --> pdb=" O TYR I 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA I 215 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG I 217 " --> pdb=" O ASP I 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP I 239 " --> pdb=" O ARG I 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE I 219 " --> pdb=" O ARG I 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG I 237 " --> pdb=" O PHE I 219 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'I' and resid 301 through 305 removed outlier: 3.690A pdb=" N VAL I 303 " --> pdb=" O LYS I 337 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'J' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY J 126 " --> pdb=" O TYR J 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE J 127 " --> pdb=" O CYS J 257 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'J' and resid 166 through 172 removed outlier: 7.416A pdb=" N ILE J 166 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU J 181 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN J 168 " --> pdb=" O ILE J 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE J 179 " --> pdb=" O ASN J 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG J 170 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE J 179 " --> pdb=" O LEU J 206 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR J 201 " --> pdb=" O TYR J 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA J 215 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG J 217 " --> pdb=" O ASP J 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP J 239 " --> pdb=" O ARG J 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE J 219 " --> pdb=" O ARG J 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG J 237 " --> pdb=" O PHE J 219 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'J' and resid 301 through 305 removed outlier: 3.689A pdb=" N VAL J 303 " --> pdb=" O LYS J 337 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'K' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY K 126 " --> pdb=" O TYR K 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE K 127 " --> pdb=" O CYS K 257 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'K' and resid 166 through 172 removed outlier: 7.417A pdb=" N ILE K 166 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU K 181 " --> pdb=" O ILE K 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN K 168 " --> pdb=" O ILE K 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE K 179 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG K 170 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE K 179 " --> pdb=" O LEU K 206 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR K 201 " --> pdb=" O TYR K 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA K 215 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG K 217 " --> pdb=" O ASP K 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP K 239 " --> pdb=" O ARG K 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE K 219 " --> pdb=" O ARG K 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG K 237 " --> pdb=" O PHE K 219 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'K' and resid 301 through 305 removed outlier: 3.689A pdb=" N VAL K 303 " --> pdb=" O LYS K 337 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'L' and resid 157 through 161 removed outlier: 3.506A pdb=" N GLY L 126 " --> pdb=" O TYR L 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE L 127 " --> pdb=" O CYS L 257 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'L' and resid 166 through 172 removed outlier: 7.417A pdb=" N ILE L 166 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU L 181 " --> pdb=" O ILE L 166 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN L 168 " --> pdb=" O ILE L 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE L 179 " --> pdb=" O ASN L 168 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG L 170 " --> pdb=" O THR L 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE L 179 " --> pdb=" O LEU L 206 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR L 201 " --> pdb=" O TYR L 220 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA L 215 " --> pdb=" O VAL L 241 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG L 217 " --> pdb=" O ASP L 239 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP L 239 " --> pdb=" O ARG L 217 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE L 219 " --> pdb=" O ARG L 237 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG L 237 " --> pdb=" O PHE L 219 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'L' and resid 301 through 305 removed outlier: 3.690A pdb=" N VAL L 303 " --> pdb=" O LYS L 337 " (cutoff:3.500A) 1980 hydrogen bonds defined for protein. 5724 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 5472 1.29 - 1.35: 5436 1.35 - 1.41: 0 1.41 - 1.47: 5448 1.47 - 1.53: 5496 Bond restraints: 21852 Sorted by residual: bond pdb=" CA TYR C 131 " pdb=" C TYR C 131 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.08e-02 8.57e+03 1.01e+00 bond pdb=" CA TYR I 131 " pdb=" C TYR I 131 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.08e-02 8.57e+03 1.01e+00 bond pdb=" CA TYR L 131 " pdb=" C TYR L 131 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.08e-02 8.57e+03 1.01e+00 bond pdb=" CA TYR F 131 " pdb=" C TYR F 131 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.08e-02 8.57e+03 1.01e+00 bond pdb=" CA TYR E 131 " pdb=" C TYR E 131 " ideal model delta sigma weight residual 1.530 1.520 0.011 1.08e-02 8.57e+03 9.96e-01 ... (remaining 21847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 25080 1.11 - 2.22: 1848 2.22 - 3.33: 264 3.33 - 4.44: 48 4.44 - 5.55: 12 Bond angle restraints: 27252 Sorted by residual: angle pdb=" N GLY F 362 " pdb=" CA GLY F 362 " pdb=" C GLY F 362 " ideal model delta sigma weight residual 115.43 111.57 3.86 1.41e+00 5.03e-01 7.49e+00 angle pdb=" N GLY L 362 " pdb=" CA GLY L 362 " pdb=" C GLY L 362 " ideal model delta sigma weight residual 115.43 111.57 3.86 1.41e+00 5.03e-01 7.49e+00 angle pdb=" N GLY I 362 " pdb=" CA GLY I 362 " pdb=" C GLY I 362 " ideal model delta sigma weight residual 115.43 111.57 3.86 1.41e+00 5.03e-01 7.49e+00 angle pdb=" N GLY C 362 " pdb=" CA GLY C 362 " pdb=" C GLY C 362 " ideal model delta sigma weight residual 115.43 111.57 3.86 1.41e+00 5.03e-01 7.49e+00 angle pdb=" N GLY K 362 " pdb=" CA GLY K 362 " pdb=" C GLY K 362 " ideal model delta sigma weight residual 115.43 111.60 3.83 1.41e+00 5.03e-01 7.39e+00 ... (remaining 27247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.03: 4204 3.03 - 6.05: 968 6.05 - 9.08: 204 9.08 - 12.10: 36 12.10 - 15.13: 24 Dihedral angle restraints: 5436 sinusoidal: 0 harmonic: 5436 Sorted by residual: dihedral pdb=" CA ARG D 155 " pdb=" C ARG D 155 " pdb=" N PRO D 156 " pdb=" CA PRO D 156 " ideal model delta harmonic sigma weight residual 180.00 164.87 15.13 0 5.00e+00 4.00e-02 9.16e+00 dihedral pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N PRO A 156 " pdb=" CA PRO A 156 " ideal model delta harmonic sigma weight residual 180.00 164.87 15.13 0 5.00e+00 4.00e-02 9.16e+00 dihedral pdb=" CA ARG J 155 " pdb=" C ARG J 155 " pdb=" N PRO J 156 " pdb=" CA PRO J 156 " ideal model delta harmonic sigma weight residual 180.00 164.87 15.13 0 5.00e+00 4.00e-02 9.16e+00 ... (remaining 5433 not shown) Chirality restraints: 0 Planarity restraints: 5436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 69 " -0.002 2.00e-02 2.50e+03 3.39e-03 1.15e-01 pdb=" C ALA G 69 " 0.006 2.00e-02 2.50e+03 pdb=" O ALA G 69 " -0.002 2.00e-02 2.50e+03 pdb=" N THR G 70 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 69 " 0.002 2.00e-02 2.50e+03 3.39e-03 1.15e-01 pdb=" C ALA J 69 " -0.006 2.00e-02 2.50e+03 pdb=" O ALA J 69 " 0.002 2.00e-02 2.50e+03 pdb=" N THR J 70 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 69 " -0.002 2.00e-02 2.50e+03 3.39e-03 1.15e-01 pdb=" C ALA D 69 " 0.006 2.00e-02 2.50e+03 pdb=" O ALA D 69 " -0.002 2.00e-02 2.50e+03 pdb=" N THR D 70 " -0.002 2.00e-02 2.50e+03 ... (remaining 5433 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 16920 3.04 - 3.50: 16632 3.50 - 3.97: 22062 3.97 - 4.43: 25686 4.43 - 4.90: 33224 Nonbonded interactions: 114524 Sorted by model distance: nonbonded pdb=" O GLN I 408 " pdb=" O THR I 411 " model vdw 2.575 3.040 nonbonded pdb=" O GLN L 408 " pdb=" O THR L 411 " model vdw 2.575 3.040 nonbonded pdb=" O GLN C 408 " pdb=" O THR C 411 " model vdw 2.575 3.040 nonbonded pdb=" O GLN F 408 " pdb=" O THR F 411 " model vdw 2.575 3.040 nonbonded pdb=" O GLN K 408 " pdb=" O THR K 411 " model vdw 2.575 3.040 ... (remaining 114519 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: 0.15 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.280 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 0.012 21852 Z= 0.140 Angle : 0.627 5.554 27252 Z= 0.455 Chirality : 0.000 0.000 0 Planarity : 0.001 0.003 5436 Dihedral : 2.963 15.130 5436 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.33 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.95 (0.13), residues: 5400 helix: 2.80 (0.12), residues: 2316 sheet: -0.58 (0.19), residues: 816 loop : -1.29 (0.14), residues: 2268 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.14 (21852) covalent geometry : angle 0.62689 / 0.45 (27252) hydrogen bonds : bond 0.18893 / 14.97 ( 1980) hydrogen bonds : angle 7.71982 / 6.41 ( 5724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.832 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0861 time to fit residues: 28.8486 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 30.0000 chunk 41 optimal weight: 0.0570 chunk 265 optimal weight: 40.0000 chunk 523 optimal weight: 30.0000 chunk 497 optimal weight: 0.0040 chunk 414 optimal weight: 0.8980 chunk 310 optimal weight: 30.0000 chunk 488 optimal weight: 30.0000 chunk 366 optimal weight: 30.0000 chunk 223 optimal weight: 30.0000 overall best weight: 12.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.070577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.056697 restraints weight = 127710.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.057110 restraints weight = 111167.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.057409 restraints weight = 100140.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.057559 restraints weight = 92899.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.057738 restraints weight = 88654.391| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21852 Z= 0.273 Angle : 0.591 7.218 27252 Z= 0.379 Chirality : 0.000 0.000 0 Planarity : 0.003 0.013 5436 Dihedral : 4.489 19.827 5436 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.63 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.32 (0.12), residues: 5400 helix: 1.98 (0.12), residues: 2352 sheet: -0.30 (0.19), residues: 744 loop : -1.57 (0.14), residues: 2304 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.27 (21852) covalent geometry : angle 0.59088 / 0.38 (27252) hydrogen bonds : bond 0.04371 / 3.46 ( 1980) hydrogen bonds : angle 6.57003 / 5.44 ( 5724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.913 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0898 time to fit residues: 29.9591 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 384 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 chunk 401 optimal weight: 30.0000 chunk 41 optimal weight: 0.2980 chunk 470 optimal weight: 40.0000 chunk 72 optimal weight: 40.0000 chunk 436 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 21 optimal weight: 50.0000 chunk 263 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 overall best weight: 4.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.074076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.059938 restraints weight = 125952.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060397 restraints weight = 108784.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.060643 restraints weight = 97458.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060931 restraints weight = 90652.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.061112 restraints weight = 85467.399| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.024 21852 Z= 0.106 Angle : 0.394 7.259 27252 Z= 0.232 Chirality : 0.000 0.000 0 Planarity : 0.002 0.007 5436 Dihedral : 3.574 16.002 5436 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.33 % Favored : 92.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.91 (0.13), residues: 5400 helix: 2.80 (0.12), residues: 2364 sheet: -0.86 (0.18), residues: 876 loop : -1.33 (0.15), residues: 2160 Details of bonding type rmsd/Z covalent geometry : bond 0.00148 / 0.11 (21852) covalent geometry : angle 0.39381 / 0.23 (27252) hydrogen bonds : bond 0.03057 / 2.42 ( 1980) hydrogen bonds : angle 4.98926 / 4.12 ( 5724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.892 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0898 time to fit residues: 29.9502 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 251 optimal weight: 20.0000 chunk 165 optimal weight: 0.0370 chunk 368 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 55 optimal weight: 40.0000 chunk 60 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 388 optimal weight: 40.0000 chunk 462 optimal weight: 40.0000 overall best weight: 9.5868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.055903 restraints weight = 128426.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.056339 restraints weight = 110830.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.056605 restraints weight = 99072.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.056843 restraints weight = 91844.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.057005 restraints weight = 86833.585| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21852 Z= 0.204 Angle : 0.526 7.811 27252 Z= 0.325 Chirality : 0.000 0.000 0 Planarity : 0.003 0.010 5436 Dihedral : 4.285 19.039 5436 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.85 % Favored : 89.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.50 (0.13), residues: 5400 helix: 2.38 (0.12), residues: 2364 sheet: -0.99 (0.19), residues: 744 loop : -1.47 (0.14), residues: 2292 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.20 (21852) covalent geometry : angle 0.52637 / 0.32 (27252) hydrogen bonds : bond 0.03806 / 3.02 ( 1980) hydrogen bonds : angle 5.71906 / 4.73 ( 5724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.908 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0897 time to fit residues: 30.0261 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 338 optimal weight: 50.0000 chunk 16 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 421 optimal weight: 5.9990 chunk 482 optimal weight: 20.0000 chunk 366 optimal weight: 0.0070 chunk 153 optimal weight: 50.0000 chunk 328 optimal weight: 50.0000 overall best weight: 7.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.056677 restraints weight = 127929.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.057093 restraints weight = 110120.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.057433 restraints weight = 98587.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.057656 restraints weight = 90646.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.057756 restraints weight = 85629.825| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21852 Z= 0.174 Angle : 0.465 8.270 27252 Z= 0.280 Chirality : 0.000 0.000 0 Planarity : 0.002 0.009 5436 Dihedral : 3.923 17.888 5436 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.19 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.82 (0.13), residues: 5400 helix: 2.84 (0.12), residues: 2292 sheet: -1.08 (0.19), residues: 744 loop : -1.30 (0.14), residues: 2364 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.17 (21852) covalent geometry : angle 0.46528 / 0.28 (27252) hydrogen bonds : bond 0.03178 / 2.52 ( 1980) hydrogen bonds : angle 5.06046 / 4.18 ( 5724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.883 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0899 time to fit residues: 29.9836 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 184 optimal weight: 8.9990 chunk 117 optimal weight: 0.0170 chunk 245 optimal weight: 50.0000 chunk 326 optimal weight: 7.9990 chunk 461 optimal weight: 7.9990 chunk 294 optimal weight: 0.5980 chunk 277 optimal weight: 30.0000 chunk 214 optimal weight: 50.0000 chunk 262 optimal weight: 40.0000 chunk 211 optimal weight: 4.9990 chunk 481 optimal weight: 50.0000 overall best weight: 4.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.058403 restraints weight = 126932.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.058852 restraints weight = 109042.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.059188 restraints weight = 97372.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.059401 restraints weight = 89480.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.059586 restraints weight = 84529.952| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.022 21852 Z= 0.104 Angle : 0.363 6.742 27252 Z= 0.213 Chirality : 0.000 0.000 0 Planarity : 0.001 0.007 5436 Dihedral : 3.417 17.189 5436 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.52 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.15 (0.13), residues: 5400 helix: 3.28 (0.12), residues: 2292 sheet: -1.16 (0.18), residues: 864 loop : -1.20 (0.15), residues: 2244 Details of bonding type rmsd/Z covalent geometry : bond 0.00146 / 0.10 (21852) covalent geometry : angle 0.36318 / 0.21 (27252) hydrogen bonds : bond 0.02591 / 2.05 ( 1980) hydrogen bonds : angle 4.44551 / 3.67 ( 5724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.891 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0894 time to fit residues: 29.8848 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 327 optimal weight: 30.0000 chunk 429 optimal weight: 3.9990 chunk 432 optimal weight: 5.9990 chunk 387 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 chunk 498 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 297 optimal weight: 30.0000 chunk 79 optimal weight: 50.0000 chunk 383 optimal weight: 50.0000 chunk 373 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.071090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.057144 restraints weight = 127515.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.057596 restraints weight = 109614.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.057869 restraints weight = 97688.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.058115 restraints weight = 90608.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.058293 restraints weight = 85233.563| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21852 Z= 0.142 Angle : 0.393 6.413 27252 Z= 0.238 Chirality : 0.000 0.000 0 Planarity : 0.002 0.008 5436 Dihedral : 3.617 18.393 5436 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.85 % Favored : 89.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.19 (0.13), residues: 5400 helix: 3.26 (0.12), residues: 2292 sheet: -1.11 (0.18), residues: 852 loop : -1.14 (0.15), residues: 2256 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.14 (21852) covalent geometry : angle 0.39275 / 0.24 (27252) hydrogen bonds : bond 0.02866 / 2.27 ( 1980) hydrogen bonds : angle 4.69216 / 3.87 ( 5724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.765 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0894 time to fit residues: 29.9958 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 128 optimal weight: 30.0000 chunk 476 optimal weight: 7.9990 chunk 404 optimal weight: 0.0870 chunk 250 optimal weight: 30.0000 chunk 255 optimal weight: 30.0000 chunk 426 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 525 optimal weight: 0.0980 chunk 111 optimal weight: 30.0000 chunk 153 optimal weight: 50.0000 overall best weight: 9.6368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.068715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.054988 restraints weight = 128925.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.055387 restraints weight = 110590.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.055720 restraints weight = 98809.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.055940 restraints weight = 91000.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.056047 restraints weight = 85713.414| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21852 Z= 0.214 Angle : 0.488 6.887 27252 Z= 0.305 Chirality : 0.000 0.000 0 Planarity : 0.002 0.009 5436 Dihedral : 4.131 18.792 5436 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.31 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.72 (0.13), residues: 5400 helix: 2.77 (0.12), residues: 2292 sheet: -1.24 (0.18), residues: 852 loop : -1.31 (0.15), residues: 2256 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.21 (21852) covalent geometry : angle 0.48794 / 0.30 (27252) hydrogen bonds : bond 0.03416 / 2.71 ( 1980) hydrogen bonds : angle 5.32153 / 4.39 ( 5724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.902 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0893 time to fit residues: 29.8815 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 487 optimal weight: 40.0000 chunk 24 optimal weight: 0.0040 chunk 432 optimal weight: 40.0000 chunk 137 optimal weight: 30.0000 chunk 318 optimal weight: 4.9990 chunk 358 optimal weight: 40.0000 chunk 186 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 389 optimal weight: 7.9990 chunk 293 optimal weight: 50.0000 chunk 94 optimal weight: 6.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.071647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.057596 restraints weight = 127849.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.058077 restraints weight = 108751.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.058398 restraints weight = 96239.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.058596 restraints weight = 88426.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.058793 restraints weight = 83576.478| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 21852 Z= 0.103 Angle : 0.344 4.932 27252 Z= 0.207 Chirality : 0.000 0.000 0 Planarity : 0.001 0.006 5436 Dihedral : 3.402 16.241 5436 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.37 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.22 (0.13), residues: 5400 helix: 3.34 (0.12), residues: 2292 sheet: -1.17 (0.18), residues: 852 loop : -1.16 (0.15), residues: 2256 Details of bonding type rmsd/Z covalent geometry : bond 0.00145 / 0.10 (21852) covalent geometry : angle 0.34422 / 0.21 (27252) hydrogen bonds : bond 0.02564 / 2.03 ( 1980) hydrogen bonds : angle 4.42362 / 3.64 ( 5724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.853 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0890 time to fit residues: 29.5855 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 104 optimal weight: 0.9990 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 275 optimal weight: 30.0000 chunk 336 optimal weight: 30.0000 chunk 212 optimal weight: 20.0000 chunk 473 optimal weight: 50.0000 chunk 47 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 50.0000 chunk 184 optimal weight: 1.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.070738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.056770 restraints weight = 128280.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.057226 restraints weight = 109066.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.057566 restraints weight = 96744.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.057713 restraints weight = 88672.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.057947 restraints weight = 84001.854| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21852 Z= 0.125 Angle : 0.356 4.046 27252 Z= 0.219 Chirality : 0.000 0.000 0 Planarity : 0.002 0.007 5436 Dihedral : 3.453 17.231 5436 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.30 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.23 (0.13), residues: 5400 helix: 3.40 (0.12), residues: 2292 sheet: -1.19 (0.18), residues: 852 loop : -1.19 (0.15), residues: 2256 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.12 (21852) covalent geometry : angle 0.35617 / 0.22 (27252) hydrogen bonds : bond 0.02670 / 2.12 ( 1980) hydrogen bonds : angle 4.56498 / 3.76 ( 5724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10800 Ramachandran restraints generated. 5400 Oldfield, 0 Emsley, 5400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.955 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0862 time to fit residues: 28.7453 Evaluate side-chains 168 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 492 optimal weight: 20.0000 chunk 475 optimal weight: 30.0000 chunk 389 optimal weight: 0.0470 chunk 440 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 139 optimal weight: 0.0980 chunk 373 optimal weight: 50.0000 chunk 412 optimal weight: 30.0000 chunk 128 optimal weight: 30.0000 chunk 419 optimal weight: 50.0000 overall best weight: 9.2288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.068354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.054603 restraints weight = 129767.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.055061 restraints weight = 110182.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.055341 restraints weight = 97603.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.055583 restraints weight = 89865.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.055680 restraints weight = 84128.116| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21852 Z= 0.209 Angle : 0.468 5.221 27252 Z= 0.299 Chirality : 0.000 0.000 0 Planarity : 0.002 0.009 5436 Dihedral : 4.052 18.862 5436 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.85 % Favored : 87.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 0.70 (0.13), residues: 5400 helix: 2.91 (0.12), residues: 2292 sheet: -1.57 (0.17), residues: 912 loop : -1.35 (0.15), residues: 2196 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.21 (21852) covalent geometry : angle 0.46802 / 0.30 (27252) hydrogen bonds : bond 0.03344 / 2.65 ( 1980) hydrogen bonds : angle 5.30958 / 4.38 ( 5724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2750.68 seconds wall clock time: 47 minutes 40.81 seconds (2860.81 seconds total)