Starting phenix.real_space_refine on Thu Jun 26 23:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xfa_22168/06_2025/6xfa_22168.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xfa_22168/06_2025/6xfa_22168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xfa_22168/06_2025/6xfa_22168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xfa_22168/06_2025/6xfa_22168.map" model { file = "/net/cci-nas-00/data/ceres_data/6xfa_22168/06_2025/6xfa_22168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xfa_22168/06_2025/6xfa_22168.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 20 6.06 5 S 240 5.16 5 C 20510 2.51 5 N 5230 2.21 5 O 5730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31730 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3171 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 400 SG CYS A 54 96.085 111.428 85.400 1.00 0.79 S ATOM 424 SG CYS A 57 95.742 113.780 82.794 1.00 0.80 S ATOM 1075 SG CYS A 138 95.274 109.880 81.114 1.00 0.71 S ATOM 1849 SG CYS A 316 111.068 88.854 85.296 1.00 0.83 S ATOM 1870 SG CYS A 319 110.130 92.188 82.780 1.00 0.84 S ATOM 2468 SG CYS A 393 108.345 89.119 83.063 1.00 0.85 S Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 9.98, per 1000 atoms: 0.31 Number of scatterers: 31730 At special positions: 0 Unit cell: (147.06, 149.34, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 20 29.99 S 240 16.00 O 5730 8.00 N 5230 7.00 C 20510 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: 8.44 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 57 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 132 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 138 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 54 " pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 386 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 319 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 316 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 393 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 57 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 132 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 138 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 54 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 386 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 319 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 316 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 393 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 57 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 132 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 138 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 54 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 386 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 319 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 316 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 393 " pdb=" ZN D 500 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 57 " pdb="ZN ZN D 500 " - pdb=" ND1 HIS D 132 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 138 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 54 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 386 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 319 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 316 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 393 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 57 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 132 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 138 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 54 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 386 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 319 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 316 " pdb="ZN ZN E 501 " - pdb=" SG CYS E 393 " pdb=" ZN F 500 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 57 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 132 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 138 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 54 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" ND1 HIS F 386 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 319 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 316 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 393 " pdb=" ZN G 500 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 57 " pdb="ZN ZN G 500 " - pdb=" ND1 HIS G 132 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 138 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 54 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" ND1 HIS G 386 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 319 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 316 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 393 " pdb=" ZN H 500 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 57 " pdb="ZN ZN H 500 " - pdb=" ND1 HIS H 132 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 138 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 54 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" ND1 HIS H 386 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 319 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 316 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 393 " pdb=" ZN I 500 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 57 " pdb="ZN ZN I 500 " - pdb=" ND1 HIS I 132 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 138 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 54 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" ND1 HIS I 386 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 319 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 316 " pdb="ZN ZN I 501 " - pdb=" SG CYS I 393 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 57 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 132 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 138 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 54 " pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" ND1 HIS J 386 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 319 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 316 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 393 " Number of angles added : 60 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7660 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 10 sheets defined 62.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 removed outlier: 3.906A pdb=" N LEU A 12 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 4.139A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 147 through 167 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU A 320 " --> pdb=" O CYS A 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.625A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 433 through 448 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.685A pdb=" N LYS A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU B 12 " --> pdb=" O THR B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 removed outlier: 3.928A pdb=" N LEU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.597A pdb=" N SER B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 4.139A pdb=" N LEU B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 147 through 167 Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.646A pdb=" N LEU B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU B 320 " --> pdb=" O CYS B 316 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY B 323 " --> pdb=" O CYS B 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 433 through 448 Processing helix chain 'B' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 removed outlier: 3.930A pdb=" N LEU C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 72 through 85 Processing helix chain 'C' and resid 90 through 109 removed outlier: 3.597A pdb=" N SER C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU C 118 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 147 through 167 Processing helix chain 'C' and resid 245 through 252 removed outlier: 3.591A pdb=" N LEU C 249 " --> pdb=" O TYR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.648A pdb=" N LEU C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU C 320 " --> pdb=" O CYS C 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY C 323 " --> pdb=" O CYS C 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 359 Processing helix chain 'C' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN C 376 " --> pdb=" O ARG C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 433 through 448 Processing helix chain 'C' and resid 454 through 470 removed outlier: 3.685A pdb=" N LYS C 460 " --> pdb=" O VAL C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.906A pdb=" N LEU D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 72 through 85 Processing helix chain 'D' and resid 90 through 109 removed outlier: 3.597A pdb=" N SER D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 147 through 167 Processing helix chain 'D' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU D 249 " --> pdb=" O TYR D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU D 300 " --> pdb=" O PRO D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU D 320 " --> pdb=" O CYS D 316 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY D 323 " --> pdb=" O CYS D 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 359 Processing helix chain 'D' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 389 Processing helix chain 'D' and resid 390 through 400 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.645A pdb=" N LEU D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 removed outlier: 3.802A pdb=" N THR D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 25 removed outlier: 3.930A pdb=" N LEU E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 54 through 65 Processing helix chain 'E' and resid 72 through 85 Processing helix chain 'E' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 removed outlier: 4.139A pdb=" N LEU E 118 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 147 through 167 Processing helix chain 'E' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 325 removed outlier: 3.532A pdb=" N GLU E 320 " --> pdb=" O CYS E 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY E 323 " --> pdb=" O CYS E 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 359 Processing helix chain 'E' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 389 Processing helix chain 'E' and resid 390 through 400 Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 413 through 423 Processing helix chain 'E' and resid 433 through 448 Processing helix chain 'E' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS E 460 " --> pdb=" O VAL E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 482 removed outlier: 3.804A pdb=" N THR E 479 " --> pdb=" O GLN E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU F 12 " --> pdb=" O THR F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 54 through 65 Processing helix chain 'F' and resid 72 through 85 Processing helix chain 'F' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU F 118 " --> pdb=" O LEU F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 147 through 167 Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU F 249 " --> pdb=" O TYR F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU F 300 " --> pdb=" O PRO F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU F 320 " --> pdb=" O CYS F 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY F 323 " --> pdb=" O CYS F 319 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS F 325 " --> pdb=" O SER F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 359 Processing helix chain 'F' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 389 Processing helix chain 'F' and resid 390 through 400 Processing helix chain 'F' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU F 405 " --> pdb=" O ASN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 413 through 423 Processing helix chain 'F' and resid 433 through 448 Processing helix chain 'F' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS F 460 " --> pdb=" O VAL F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR F 479 " --> pdb=" O GLN F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU G 12 " --> pdb=" O THR G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 54 through 65 Processing helix chain 'G' and resid 72 through 85 Processing helix chain 'G' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 147 through 167 Processing helix chain 'G' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 325 removed outlier: 3.530A pdb=" N GLU G 320 " --> pdb=" O CYS G 316 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY G 323 " --> pdb=" O CYS G 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS G 325 " --> pdb=" O SER G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 359 Processing helix chain 'G' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN G 376 " --> pdb=" O ARG G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 389 Processing helix chain 'G' and resid 390 through 400 Processing helix chain 'G' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU G 405 " --> pdb=" O ASN G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 412 No H-bonds generated for 'chain 'G' and resid 410 through 412' Processing helix chain 'G' and resid 413 through 423 Processing helix chain 'G' and resid 433 through 448 Processing helix chain 'G' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS G 460 " --> pdb=" O VAL G 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 482 removed outlier: 3.802A pdb=" N THR G 479 " --> pdb=" O GLN G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU H 12 " --> pdb=" O THR H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 25 removed outlier: 3.930A pdb=" N LEU H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 54 through 65 Processing helix chain 'H' and resid 72 through 85 Processing helix chain 'H' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 removed outlier: 4.139A pdb=" N LEU H 118 " --> pdb=" O LEU H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 147 through 167 Processing helix chain 'H' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU H 249 " --> pdb=" O TYR H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU H 300 " --> pdb=" O PRO H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU H 320 " --> pdb=" O CYS H 316 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY H 323 " --> pdb=" O CYS H 319 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS H 325 " --> pdb=" O SER H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR H 331 " --> pdb=" O ASP H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 359 Processing helix chain 'H' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN H 376 " --> pdb=" O ARG H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 389 Processing helix chain 'H' and resid 390 through 400 Processing helix chain 'H' and resid 401 through 406 removed outlier: 3.645A pdb=" N LEU H 405 " --> pdb=" O ASN H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 412 No H-bonds generated for 'chain 'H' and resid 410 through 412' Processing helix chain 'H' and resid 413 through 423 Processing helix chain 'H' and resid 433 through 448 Processing helix chain 'H' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS H 460 " --> pdb=" O VAL H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 482 removed outlier: 3.804A pdb=" N THR H 479 " --> pdb=" O GLN H 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 14 removed outlier: 3.906A pdb=" N LEU I 12 " --> pdb=" O THR I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 48 Processing helix chain 'I' and resid 54 through 65 Processing helix chain 'I' and resid 72 through 85 Processing helix chain 'I' and resid 90 through 109 removed outlier: 3.597A pdb=" N SER I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU I 118 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 134 Processing helix chain 'I' and resid 147 through 167 Processing helix chain 'I' and resid 245 through 252 removed outlier: 3.592A pdb=" N LEU I 249 " --> pdb=" O TYR I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 301 removed outlier: 3.646A pdb=" N LEU I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU I 320 " --> pdb=" O CYS I 316 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY I 323 " --> pdb=" O CYS I 319 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS I 325 " --> pdb=" O SER I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR I 331 " --> pdb=" O ASP I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 348 through 359 Processing helix chain 'I' and resid 368 through 376 removed outlier: 3.513A pdb=" N GLN I 376 " --> pdb=" O ARG I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 379 through 389 Processing helix chain 'I' and resid 390 through 400 Processing helix chain 'I' and resid 401 through 406 removed outlier: 3.644A pdb=" N LEU I 405 " --> pdb=" O ASN I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 412 No H-bonds generated for 'chain 'I' and resid 410 through 412' Processing helix chain 'I' and resid 413 through 423 Processing helix chain 'I' and resid 433 through 448 Processing helix chain 'I' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS I 460 " --> pdb=" O VAL I 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR I 479 " --> pdb=" O GLN I 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 14 removed outlier: 3.907A pdb=" N LEU J 12 " --> pdb=" O THR J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 25 removed outlier: 3.929A pdb=" N LEU J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 48 Processing helix chain 'J' and resid 54 through 65 Processing helix chain 'J' and resid 72 through 85 Processing helix chain 'J' and resid 90 through 109 removed outlier: 3.598A pdb=" N SER J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 118 removed outlier: 4.138A pdb=" N LEU J 118 " --> pdb=" O LEU J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 147 through 167 Processing helix chain 'J' and resid 245 through 252 removed outlier: 3.593A pdb=" N LEU J 249 " --> pdb=" O TYR J 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 removed outlier: 3.647A pdb=" N LEU J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 325 removed outlier: 3.531A pdb=" N GLU J 320 " --> pdb=" O CYS J 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY J 323 " --> pdb=" O CYS J 319 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS J 325 " --> pdb=" O SER J 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 342 removed outlier: 3.626A pdb=" N THR J 331 " --> pdb=" O ASP J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 359 Processing helix chain 'J' and resid 368 through 376 removed outlier: 3.514A pdb=" N GLN J 376 " --> pdb=" O ARG J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 389 Processing helix chain 'J' and resid 390 through 400 Processing helix chain 'J' and resid 401 through 406 removed outlier: 3.645A pdb=" N LEU J 405 " --> pdb=" O ASN J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 412 No H-bonds generated for 'chain 'J' and resid 410 through 412' Processing helix chain 'J' and resid 413 through 423 Processing helix chain 'J' and resid 433 through 448 Processing helix chain 'J' and resid 454 through 470 removed outlier: 3.686A pdb=" N LYS J 460 " --> pdb=" O VAL J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 482 removed outlier: 3.803A pdb=" N THR J 479 " --> pdb=" O GLN J 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA2, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA3, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA4, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'E' and resid 308 through 309 Processing sheet with id=AA6, first strand: chain 'F' and resid 308 through 309 Processing sheet with id=AA7, first strand: chain 'G' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'H' and resid 308 through 309 Processing sheet with id=AA9, first strand: chain 'I' and resid 308 through 309 Processing sheet with id=AB1, first strand: chain 'J' and resid 308 through 309 1530 hydrogen bonds defined for protein. 4500 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: 10.53 Time building geometry restraints manager: 9.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10070 1.34 - 1.46: 7348 1.46 - 1.58: 14772 1.58 - 1.70: 0 1.70 - 1.81: 320 Bond restraints: 32510 Sorted by residual: bond pdb=" CB TRP E 91 " pdb=" CG TRP E 91 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.07e+00 bond pdb=" CB TRP B 91 " pdb=" CG TRP B 91 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.05e+00 bond pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.03e+00 bond pdb=" CB TRP C 91 " pdb=" CG TRP C 91 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.03e+00 bond pdb=" CB TRP G 91 " pdb=" CG TRP G 91 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.03e+00 ... (remaining 32505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 42730 1.53 - 3.07: 1255 3.07 - 4.60: 205 4.60 - 6.14: 50 6.14 - 7.67: 20 Bond angle restraints: 44260 Sorted by residual: angle pdb=" CA CYS E 136 " pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " ideal model delta sigma weight residual 114.40 119.93 -5.53 2.30e+00 1.89e-01 5.79e+00 angle pdb=" CA CYS C 136 " pdb=" CB CYS C 136 " pdb=" SG CYS C 136 " ideal model delta sigma weight residual 114.40 119.91 -5.51 2.30e+00 1.89e-01 5.73e+00 angle pdb=" CA CYS F 136 " pdb=" CB CYS F 136 " pdb=" SG CYS F 136 " ideal model delta sigma weight residual 114.40 119.90 -5.50 2.30e+00 1.89e-01 5.72e+00 angle pdb=" CA CYS B 136 " pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " ideal model delta sigma weight residual 114.40 119.89 -5.49 2.30e+00 1.89e-01 5.70e+00 angle pdb=" CA CYS D 136 " pdb=" CB CYS D 136 " pdb=" SG CYS D 136 " ideal model delta sigma weight residual 114.40 119.88 -5.48 2.30e+00 1.89e-01 5.68e+00 ... (remaining 44255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 17047 16.78 - 33.56: 1846 33.56 - 50.33: 367 50.33 - 67.11: 30 67.11 - 83.89: 40 Dihedral angle restraints: 19330 sinusoidal: 7490 harmonic: 11840 Sorted by residual: dihedral pdb=" CA CYS G 389 " pdb=" C CYS G 389 " pdb=" N ASP G 390 " pdb=" CA ASP G 390 " ideal model delta harmonic sigma weight residual -180.00 -164.63 -15.37 0 5.00e+00 4.00e-02 9.45e+00 dihedral pdb=" CA CYS A 389 " pdb=" C CYS A 389 " pdb=" N ASP A 390 " pdb=" CA ASP A 390 " ideal model delta harmonic sigma weight residual -180.00 -164.66 -15.34 0 5.00e+00 4.00e-02 9.41e+00 dihedral pdb=" CA CYS I 389 " pdb=" C CYS I 389 " pdb=" N ASP I 390 " pdb=" CA ASP I 390 " ideal model delta harmonic sigma weight residual -180.00 -164.69 -15.31 0 5.00e+00 4.00e-02 9.37e+00 ... (remaining 19327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2413 0.028 - 0.057: 1683 0.057 - 0.085: 656 0.085 - 0.114: 241 0.114 - 0.142: 87 Chirality restraints: 5080 Sorted by residual: chirality pdb=" CA ASP J 68 " pdb=" N ASP J 68 " pdb=" C ASP J 68 " pdb=" CB ASP J 68 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ASP D 68 " pdb=" N ASP D 68 " pdb=" C ASP D 68 " pdb=" CB ASP D 68 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASP G 68 " pdb=" N ASP G 68 " pdb=" C ASP G 68 " pdb=" CB ASP G 68 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 5077 not shown) Planarity restraints: 5620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 38 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO H 39 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 39 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 39 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 38 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO D 39 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " 0.026 5.00e-02 4.00e+02 ... (remaining 5617 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4269 2.74 - 3.28: 31028 3.28 - 3.82: 49304 3.82 - 4.36: 57958 4.36 - 4.90: 100777 Nonbonded interactions: 243336 Sorted by model distance: nonbonded pdb=" OG1 THR J 359 " pdb=" OE1 GLN J 360 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR C 359 " pdb=" OE1 GLN C 360 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR H 359 " pdb=" OE1 GLN H 360 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR D 359 " pdb=" OE1 GLN D 360 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR I 359 " pdb=" OE1 GLN I 360 " model vdw 2.205 3.040 ... (remaining 243331 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: 0.30 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.230 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 68.260 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.010 0.338 32590 Z= 0.316 Angle : 0.935 24.492 44320 Z= 0.392 Chirality : 0.045 0.142 5080 Planarity : 0.005 0.048 5620 Dihedral : 14.344 83.890 11670 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.57 % Allowed : 3.85 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.11), residues: 4000 helix: -1.43 (0.10), residues: 2320 sheet: None (None), residues: 0 loop : -4.04 (0.12), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 91 HIS 0.003 0.001 HIS E 43 PHE 0.011 0.001 PHE D 160 TYR 0.010 0.001 TYR B 440 ARG 0.001 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.13055 ( 1530) hydrogen bonds : angle 5.80801 ( 4500) metal coordination : bond 0.15706 ( 80) metal coordination : angle 17.92857 ( 60) covalent geometry : bond 0.00561 (32510) covalent geometry : angle 0.66261 (44260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 492 time to evaluate : 4.262 Fit side-chains REVERT: A 17 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 298 CYS cc_start: 0.8245 (m) cc_final: 0.8009 (m) REVERT: A 399 ILE cc_start: 0.8848 (tt) cc_final: 0.8556 (tt) REVERT: B 146 ASP cc_start: 0.7630 (t70) cc_final: 0.7129 (t70) REVERT: B 364 LEU cc_start: 0.7827 (mt) cc_final: 0.7596 (mt) REVERT: B 399 ILE cc_start: 0.8947 (tt) cc_final: 0.8688 (tt) REVERT: C 399 ILE cc_start: 0.8677 (tt) cc_final: 0.8356 (tt) REVERT: D 399 ILE cc_start: 0.8800 (tt) cc_final: 0.8552 (tt) REVERT: E 147 MET cc_start: 0.7190 (mmm) cc_final: 0.6964 (mmm) REVERT: E 178 MET cc_start: 0.6709 (mtt) cc_final: 0.6506 (mtt) REVERT: E 399 ILE cc_start: 0.8838 (tt) cc_final: 0.8524 (tt) REVERT: F 399 ILE cc_start: 0.8686 (tt) cc_final: 0.8371 (tt) REVERT: G 399 ILE cc_start: 0.8801 (tt) cc_final: 0.8564 (tt) REVERT: H 147 MET cc_start: 0.7206 (mmm) cc_final: 0.6962 (mmm) REVERT: H 399 ILE cc_start: 0.8813 (tt) cc_final: 0.8490 (tt) REVERT: I 298 CYS cc_start: 0.8388 (m) cc_final: 0.8087 (m) REVERT: I 399 ILE cc_start: 0.8809 (tt) cc_final: 0.8505 (tt) outliers start: 20 outliers final: 0 residues processed: 502 average time/residue: 0.4417 time to fit residues: 358.3680 Evaluate side-chains 391 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 7.9990 chunk 303 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 363 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN B 65 ASN B 150 ASN C 15 GLN C 150 ASN D 65 ASN D 150 ASN E 150 ASN F 15 GLN F 150 ASN G 15 GLN G 150 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN I 15 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN J 150 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.122516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.103264 restraints weight = 40710.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.104602 restraints weight = 33877.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.105708 restraints weight = 29731.004| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32590 Z= 0.139 Angle : 0.602 9.623 44320 Z= 0.303 Chirality : 0.042 0.153 5080 Planarity : 0.005 0.054 5620 Dihedral : 4.586 18.986 4330 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.00 % Allowed : 11.42 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.13), residues: 4000 helix: -0.20 (0.11), residues: 2330 sheet: None (None), residues: 0 loop : -3.18 (0.13), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 91 HIS 0.006 0.001 HIS J 132 PHE 0.018 0.001 PHE A 16 TYR 0.012 0.001 TYR I 134 ARG 0.003 0.000 ARG E 467 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 1530) hydrogen bonds : angle 4.39809 ( 4500) metal coordination : bond 0.00558 ( 80) metal coordination : angle 2.61467 ( 60) covalent geometry : bond 0.00331 (32510) covalent geometry : angle 0.59490 (44260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 450 time to evaluate : 3.852 Fit side-chains revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7289 (tt) REVERT: A 320 GLU cc_start: 0.8453 (mp0) cc_final: 0.8223 (mp0) REVERT: A 399 ILE cc_start: 0.8844 (tt) cc_final: 0.8503 (tt) REVERT: B 7 TRP cc_start: 0.7817 (m100) cc_final: 0.7456 (m100) REVERT: B 128 ASP cc_start: 0.8444 (m-30) cc_final: 0.8234 (m-30) REVERT: B 146 ASP cc_start: 0.8000 (t70) cc_final: 0.7754 (t70) REVERT: B 320 GLU cc_start: 0.8476 (mp0) cc_final: 0.8084 (mt-10) REVERT: B 360 GLN cc_start: 0.7810 (pm20) cc_final: 0.7584 (pm20) REVERT: B 399 ILE cc_start: 0.8890 (tt) cc_final: 0.8588 (tt) REVERT: C 146 ASP cc_start: 0.8263 (t70) cc_final: 0.7957 (t0) REVERT: C 303 MET cc_start: 0.8628 (mmm) cc_final: 0.8345 (mmt) REVERT: C 399 ILE cc_start: 0.8824 (tt) cc_final: 0.8509 (tt) REVERT: D 399 ILE cc_start: 0.8928 (tt) cc_final: 0.8663 (tt) REVERT: E 321 SER cc_start: 0.9329 (m) cc_final: 0.9086 (p) REVERT: E 360 GLN cc_start: 0.7697 (pm20) cc_final: 0.7425 (pt0) REVERT: E 399 ILE cc_start: 0.8869 (tt) cc_final: 0.8523 (tt) REVERT: F 399 ILE cc_start: 0.8827 (tt) cc_final: 0.8519 (tt) REVERT: G 360 GLN cc_start: 0.7991 (pm20) cc_final: 0.7786 (pm20) REVERT: G 399 ILE cc_start: 0.8933 (tt) cc_final: 0.8657 (tt) REVERT: H 146 ASP cc_start: 0.8370 (t70) cc_final: 0.8080 (t70) REVERT: H 321 SER cc_start: 0.9328 (m) cc_final: 0.9087 (p) REVERT: H 360 GLN cc_start: 0.7667 (pm20) cc_final: 0.7347 (pt0) REVERT: H 399 ILE cc_start: 0.8868 (tt) cc_final: 0.8528 (tt) REVERT: I 320 GLU cc_start: 0.8449 (mp0) cc_final: 0.8221 (mp0) REVERT: I 360 GLN cc_start: 0.7855 (pm20) cc_final: 0.7527 (pm20) REVERT: I 399 ILE cc_start: 0.8849 (tt) cc_final: 0.8544 (tt) REVERT: J 128 ASP cc_start: 0.8485 (m-30) cc_final: 0.8258 (m-30) REVERT: J 146 ASP cc_start: 0.8015 (t70) cc_final: 0.7766 (t70) REVERT: J 259 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6990 (tt) REVERT: J 320 GLU cc_start: 0.8492 (mp0) cc_final: 0.8051 (mt-10) REVERT: J 321 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.9128 (t) outliers start: 35 outliers final: 23 residues processed: 473 average time/residue: 0.4238 time to fit residues: 326.8962 Evaluate side-chains 414 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 388 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 308 HIS Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 321 SER Chi-restraints excluded: chain J residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 311 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 358 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 356 optimal weight: 0.7980 chunk 280 optimal weight: 6.9990 chunk 301 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN J 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.108219 restraints weight = 40563.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109482 restraints weight = 33089.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110770 restraints weight = 28842.879| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32590 Z= 0.104 Angle : 0.554 11.940 44320 Z= 0.273 Chirality : 0.040 0.135 5080 Planarity : 0.005 0.054 5620 Dihedral : 4.183 16.590 4330 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.31 % Allowed : 13.36 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 4000 helix: 0.28 (0.11), residues: 2400 sheet: None (None), residues: 0 loop : -2.65 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 374 HIS 0.005 0.001 HIS G 132 PHE 0.013 0.001 PHE G 160 TYR 0.011 0.001 TYR B 410 ARG 0.002 0.000 ARG J 372 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 1530) hydrogen bonds : angle 4.04011 ( 4500) metal coordination : bond 0.00446 ( 80) metal coordination : angle 2.33605 ( 60) covalent geometry : bond 0.00238 (32510) covalent geometry : angle 0.54741 (44260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 444 time to evaluate : 3.857 Fit side-chains REVERT: A 259 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7326 (tt) REVERT: A 320 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: A 399 ILE cc_start: 0.8885 (tt) cc_final: 0.8566 (tt) REVERT: B 7 TRP cc_start: 0.7675 (m100) cc_final: 0.7363 (m100) REVERT: B 128 ASP cc_start: 0.8456 (m-30) cc_final: 0.8229 (m-30) REVERT: B 146 ASP cc_start: 0.8076 (t70) cc_final: 0.7796 (t70) REVERT: B 242 LYS cc_start: 0.7650 (pttm) cc_final: 0.7261 (ptpt) REVERT: B 320 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: B 399 ILE cc_start: 0.8902 (tt) cc_final: 0.8622 (tt) REVERT: C 146 ASP cc_start: 0.8214 (t70) cc_final: 0.7860 (t0) REVERT: C 303 MET cc_start: 0.8560 (mmm) cc_final: 0.8299 (mmt) REVERT: C 399 ILE cc_start: 0.8961 (tt) cc_final: 0.8600 (tt) REVERT: D 320 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: D 399 ILE cc_start: 0.8958 (tt) cc_final: 0.8678 (tt) REVERT: E 146 ASP cc_start: 0.8301 (t70) cc_final: 0.7953 (t0) REVERT: E 147 MET cc_start: 0.6919 (mmm) cc_final: 0.6307 (mmm) REVERT: E 242 LYS cc_start: 0.7650 (pttm) cc_final: 0.7207 (ptpt) REVERT: E 399 ILE cc_start: 0.8934 (tt) cc_final: 0.8585 (tt) REVERT: F 146 ASP cc_start: 0.8284 (t0) cc_final: 0.8075 (t0) REVERT: F 303 MET cc_start: 0.8561 (mmm) cc_final: 0.8291 (mmt) REVERT: F 399 ILE cc_start: 0.8954 (tt) cc_final: 0.8591 (tt) REVERT: G 320 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: G 360 GLN cc_start: 0.7654 (pm20) cc_final: 0.7404 (pt0) REVERT: G 399 ILE cc_start: 0.8952 (tt) cc_final: 0.8678 (tt) REVERT: H 146 ASP cc_start: 0.8231 (t70) cc_final: 0.7790 (t0) REVERT: H 399 ILE cc_start: 0.8935 (tt) cc_final: 0.8592 (tt) REVERT: I 320 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: I 399 ILE cc_start: 0.8881 (tt) cc_final: 0.8582 (tt) REVERT: J 128 ASP cc_start: 0.8466 (m-30) cc_final: 0.8233 (m-30) REVERT: J 146 ASP cc_start: 0.8099 (t70) cc_final: 0.7811 (t70) REVERT: J 242 LYS cc_start: 0.7613 (pttm) cc_final: 0.7253 (ptpt) REVERT: J 259 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6962 (tt) REVERT: J 320 GLU cc_start: 0.8436 (mp0) cc_final: 0.8107 (mt-10) outliers start: 46 outliers final: 32 residues processed: 471 average time/residue: 0.4096 time to fit residues: 317.2824 Evaluate side-chains 433 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 394 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 308 HIS Chi-restraints excluded: chain G residue 320 GLU Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 293 HIS Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 306 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 305 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN G 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.126126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.106289 restraints weight = 40714.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.107975 restraints weight = 32778.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.109044 restraints weight = 28156.156| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 32590 Z= 0.106 Angle : 0.547 11.596 44320 Z= 0.268 Chirality : 0.040 0.136 5080 Planarity : 0.005 0.053 5620 Dihedral : 4.057 15.983 4330 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.03 % Rotamer: Outliers : 1.28 % Allowed : 15.67 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 4000 helix: 0.58 (0.11), residues: 2400 sheet: None (None), residues: 0 loop : -2.43 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.003 0.001 HIS G 132 PHE 0.012 0.001 PHE G 160 TYR 0.009 0.001 TYR B 410 ARG 0.007 0.000 ARG H 372 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 1530) hydrogen bonds : angle 3.92108 ( 4500) metal coordination : bond 0.00374 ( 80) metal coordination : angle 2.06160 ( 60) covalent geometry : bond 0.00249 (32510) covalent geometry : angle 0.54252 (44260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 396 time to evaluate : 3.583 Fit side-chains REVERT: A 259 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7346 (tt) REVERT: A 320 GLU cc_start: 0.8359 (mp0) cc_final: 0.8141 (mp0) REVERT: A 399 ILE cc_start: 0.8972 (tt) cc_final: 0.8628 (tt) REVERT: B 7 TRP cc_start: 0.7558 (m100) cc_final: 0.7309 (m100) REVERT: B 146 ASP cc_start: 0.8027 (t70) cc_final: 0.7689 (t70) REVERT: B 242 LYS cc_start: 0.7518 (pttm) cc_final: 0.7155 (ptpt) REVERT: B 320 GLU cc_start: 0.8431 (mp0) cc_final: 0.8078 (mt-10) REVERT: C 146 ASP cc_start: 0.8216 (t70) cc_final: 0.7859 (t0) REVERT: C 303 MET cc_start: 0.8570 (mmm) cc_final: 0.8311 (mmt) REVERT: C 399 ILE cc_start: 0.9011 (tt) cc_final: 0.8635 (tt) REVERT: D 399 ILE cc_start: 0.8980 (tt) cc_final: 0.8691 (tt) REVERT: E 146 ASP cc_start: 0.8244 (t70) cc_final: 0.7938 (t0) REVERT: E 242 LYS cc_start: 0.7482 (pttm) cc_final: 0.7059 (ptpt) REVERT: E 399 ILE cc_start: 0.8924 (tt) cc_final: 0.8594 (tt) REVERT: F 303 MET cc_start: 0.8561 (mmm) cc_final: 0.8297 (mmt) REVERT: F 399 ILE cc_start: 0.9011 (tt) cc_final: 0.8635 (tt) REVERT: G 399 ILE cc_start: 0.8984 (tt) cc_final: 0.8689 (tt) REVERT: H 146 ASP cc_start: 0.8227 (t70) cc_final: 0.7762 (t0) REVERT: H 242 LYS cc_start: 0.7472 (pttm) cc_final: 0.7054 (ptpt) REVERT: H 399 ILE cc_start: 0.8924 (tt) cc_final: 0.8598 (tt) REVERT: I 259 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7271 (tt) REVERT: I 320 GLU cc_start: 0.8412 (mp0) cc_final: 0.8195 (mp0) REVERT: I 399 ILE cc_start: 0.8988 (tt) cc_final: 0.8666 (tt) REVERT: J 146 ASP cc_start: 0.8004 (t70) cc_final: 0.7659 (t70) REVERT: J 242 LYS cc_start: 0.7487 (pttm) cc_final: 0.7127 (ptpt) REVERT: J 320 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8093 (mt-10) outliers start: 45 outliers final: 34 residues processed: 425 average time/residue: 0.4042 time to fit residues: 285.0798 Evaluate side-chains 396 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 359 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 308 HIS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 293 HIS Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 304 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 397 optimal weight: 8.9990 chunk 357 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN F 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.101626 restraints weight = 40712.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.103116 restraints weight = 33248.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.104271 restraints weight = 28857.573| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 32590 Z= 0.186 Angle : 0.617 11.944 44320 Z= 0.301 Chirality : 0.042 0.128 5080 Planarity : 0.005 0.054 5620 Dihedral : 4.318 17.246 4330 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.94 % Allowed : 16.15 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4000 helix: 0.50 (0.11), residues: 2400 sheet: None (None), residues: 0 loop : -2.44 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 7 HIS 0.005 0.001 HIS D 308 PHE 0.011 0.001 PHE B 160 TYR 0.011 0.001 TYR I 134 ARG 0.002 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 1530) hydrogen bonds : angle 4.08113 ( 4500) metal coordination : bond 0.00620 ( 80) metal coordination : angle 2.55033 ( 60) covalent geometry : bond 0.00458 (32510) covalent geometry : angle 0.61027 (44260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 372 time to evaluate : 3.764 Fit side-chains REVERT: A 242 LYS cc_start: 0.7344 (pttm) cc_final: 0.6979 (ptpt) REVERT: A 259 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7376 (tt) REVERT: A 360 GLN cc_start: 0.7503 (pt0) cc_final: 0.6711 (pt0) REVERT: B 146 ASP cc_start: 0.8175 (t70) cc_final: 0.7820 (t70) REVERT: B 242 LYS cc_start: 0.7523 (pttm) cc_final: 0.7167 (ptpt) REVERT: B 259 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7018 (tt) REVERT: B 320 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: C 399 ILE cc_start: 0.9108 (tt) cc_final: 0.8750 (tt) REVERT: D 399 ILE cc_start: 0.9031 (tt) cc_final: 0.8733 (tt) REVERT: E 146 ASP cc_start: 0.8292 (t70) cc_final: 0.7945 (t0) REVERT: E 242 LYS cc_start: 0.7501 (pttm) cc_final: 0.7057 (ptpt) REVERT: E 320 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: E 399 ILE cc_start: 0.8994 (tt) cc_final: 0.8666 (tt) REVERT: F 399 ILE cc_start: 0.9109 (tt) cc_final: 0.8754 (tt) REVERT: G 399 ILE cc_start: 0.9033 (tt) cc_final: 0.8736 (tt) REVERT: H 146 ASP cc_start: 0.8283 (t70) cc_final: 0.7839 (t0) REVERT: H 242 LYS cc_start: 0.7498 (pttm) cc_final: 0.7054 (ptpt) REVERT: H 320 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: H 399 ILE cc_start: 0.8995 (tt) cc_final: 0.8669 (tt) REVERT: I 259 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7525 (tt) REVERT: J 146 ASP cc_start: 0.8182 (t70) cc_final: 0.7797 (t70) REVERT: J 242 LYS cc_start: 0.7505 (pttm) cc_final: 0.7184 (ptpt) REVERT: J 259 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7049 (tt) REVERT: J 320 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8133 (mt-10) outliers start: 68 outliers final: 52 residues processed: 416 average time/residue: 0.3987 time to fit residues: 280.0485 Evaluate side-chains 413 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 353 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 308 HIS Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 293 HIS Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 321 SER Chi-restraints excluded: chain J residue 349 ILE Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 336 optimal weight: 2.9990 chunk 244 optimal weight: 0.0370 chunk 214 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 387 optimal weight: 0.5980 chunk 295 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN E 168 GLN F 15 GLN G 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.129913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.113160 restraints weight = 40293.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114084 restraints weight = 34991.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114584 restraints weight = 31743.168| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32590 Z= 0.093 Angle : 0.533 12.083 44320 Z= 0.261 Chirality : 0.039 0.137 5080 Planarity : 0.004 0.054 5620 Dihedral : 4.013 15.998 4330 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.68 % Allowed : 17.32 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 4000 helix: 0.79 (0.11), residues: 2410 sheet: None (None), residues: 0 loop : -2.26 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 7 HIS 0.003 0.001 HIS H 132 PHE 0.013 0.001 PHE G 160 TYR 0.007 0.001 TYR B 410 ARG 0.002 0.000 ARG J 372 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 1530) hydrogen bonds : angle 3.85427 ( 4500) metal coordination : bond 0.00330 ( 80) metal coordination : angle 1.58902 ( 60) covalent geometry : bond 0.00211 (32510) covalent geometry : angle 0.53046 (44260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 395 time to evaluate : 3.387 Fit side-chains REVERT: A 242 LYS cc_start: 0.7248 (pttm) cc_final: 0.6900 (ptpt) REVERT: A 259 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7356 (tt) REVERT: A 320 GLU cc_start: 0.8229 (mp0) cc_final: 0.7998 (mp0) REVERT: A 360 GLN cc_start: 0.7424 (pt0) cc_final: 0.6742 (pt0) REVERT: B 146 ASP cc_start: 0.7959 (t70) cc_final: 0.7577 (t70) REVERT: B 174 CYS cc_start: 0.7528 (t) cc_final: 0.7290 (t) REVERT: B 242 LYS cc_start: 0.7410 (pttm) cc_final: 0.7069 (ptpt) REVERT: B 259 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6954 (tt) REVERT: C 146 ASP cc_start: 0.8148 (t70) cc_final: 0.7764 (t0) REVERT: C 399 ILE cc_start: 0.9012 (tt) cc_final: 0.8630 (tt) REVERT: D 61 ASP cc_start: 0.7595 (m-30) cc_final: 0.7380 (m-30) REVERT: D 146 ASP cc_start: 0.8291 (t70) cc_final: 0.7976 (t0) REVERT: D 399 ILE cc_start: 0.8990 (tt) cc_final: 0.8750 (tt) REVERT: E 146 ASP cc_start: 0.8085 (t70) cc_final: 0.7725 (t0) REVERT: E 242 LYS cc_start: 0.7473 (pttm) cc_final: 0.6977 (ptpt) REVERT: E 320 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: E 399 ILE cc_start: 0.8926 (tt) cc_final: 0.8596 (tt) REVERT: F 61 ASP cc_start: 0.7826 (m-30) cc_final: 0.7613 (m-30) REVERT: F 399 ILE cc_start: 0.9017 (tt) cc_final: 0.8633 (tt) REVERT: G 61 ASP cc_start: 0.7586 (m-30) cc_final: 0.7381 (m-30) REVERT: G 99 MET cc_start: 0.8535 (mmm) cc_final: 0.8310 (mmm) REVERT: G 399 ILE cc_start: 0.8994 (tt) cc_final: 0.8748 (tt) REVERT: H 146 ASP cc_start: 0.8093 (t70) cc_final: 0.7646 (t0) REVERT: H 242 LYS cc_start: 0.7467 (pttm) cc_final: 0.6975 (ptpt) REVERT: H 259 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7220 (tt) REVERT: H 320 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: H 399 ILE cc_start: 0.8925 (tt) cc_final: 0.8599 (tt) REVERT: I 61 ASP cc_start: 0.7590 (m-30) cc_final: 0.7367 (m-30) REVERT: I 259 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7457 (tt) REVERT: I 320 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: I 399 ILE cc_start: 0.9030 (tt) cc_final: 0.8694 (tt) REVERT: J 146 ASP cc_start: 0.7973 (t70) cc_final: 0.7593 (t70) REVERT: J 174 CYS cc_start: 0.7536 (t) cc_final: 0.7288 (t) REVERT: J 242 LYS cc_start: 0.7429 (pttm) cc_final: 0.7104 (ptpt) REVERT: J 320 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8080 (mt-10) outliers start: 59 outliers final: 42 residues processed: 431 average time/residue: 0.3896 time to fit residues: 289.5550 Evaluate side-chains 418 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 368 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 308 HIS Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 293 HIS Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 207 optimal weight: 0.4980 chunk 371 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 321 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN C 15 GLN F 15 GLN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.102108 restraints weight = 40936.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.103431 restraints weight = 33942.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.104519 restraints weight = 29833.328| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 32590 Z= 0.217 Angle : 0.647 12.380 44320 Z= 0.317 Chirality : 0.043 0.144 5080 Planarity : 0.005 0.053 5620 Dihedral : 4.433 18.107 4330 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.94 % Allowed : 17.44 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 4000 helix: 0.54 (0.11), residues: 2440 sheet: None (None), residues: 0 loop : -2.43 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 7 HIS 0.005 0.001 HIS G 308 PHE 0.012 0.001 PHE A 16 TYR 0.012 0.002 TYR H 440 ARG 0.003 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 1530) hydrogen bonds : angle 4.12085 ( 4500) metal coordination : bond 0.00769 ( 80) metal coordination : angle 2.69038 ( 60) covalent geometry : bond 0.00535 (32510) covalent geometry : angle 0.64019 (44260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 360 time to evaluate : 3.338 Fit side-chains REVERT: A 242 LYS cc_start: 0.7339 (pttm) cc_final: 0.7001 (ptpt) REVERT: A 259 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7525 (tt) REVERT: B 146 ASP cc_start: 0.8198 (t70) cc_final: 0.7834 (t70) REVERT: B 242 LYS cc_start: 0.7514 (pttm) cc_final: 0.7156 (ptpt) REVERT: B 259 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7007 (tt) REVERT: C 399 ILE cc_start: 0.9123 (tt) cc_final: 0.8770 (tt) REVERT: D 399 ILE cc_start: 0.9105 (tt) cc_final: 0.8789 (tt) REVERT: E 146 ASP cc_start: 0.8365 (t70) cc_final: 0.7939 (t0) REVERT: E 242 LYS cc_start: 0.7471 (pttm) cc_final: 0.7046 (ptpt) REVERT: E 320 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: E 399 ILE cc_start: 0.9031 (tt) cc_final: 0.8721 (tt) REVERT: F 399 ILE cc_start: 0.9123 (tt) cc_final: 0.8771 (tt) REVERT: G 399 ILE cc_start: 0.9104 (tt) cc_final: 0.8795 (tt) REVERT: H 146 ASP cc_start: 0.8315 (t70) cc_final: 0.7859 (t0) REVERT: H 147 MET cc_start: 0.6986 (mmm) cc_final: 0.6557 (mmm) REVERT: H 242 LYS cc_start: 0.7462 (pttm) cc_final: 0.7035 (ptpt) REVERT: H 259 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7314 (tt) REVERT: H 320 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: H 399 ILE cc_start: 0.9030 (tt) cc_final: 0.8721 (tt) REVERT: I 259 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7608 (tt) REVERT: I 320 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: J 146 ASP cc_start: 0.8199 (t70) cc_final: 0.7778 (t70) REVERT: J 242 LYS cc_start: 0.7502 (pttm) cc_final: 0.7179 (ptpt) REVERT: J 259 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7082 (tt) REVERT: J 320 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7676 (mp0) outliers start: 68 outliers final: 55 residues processed: 405 average time/residue: 0.3740 time to fit residues: 256.2763 Evaluate side-chains 411 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 347 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 308 HIS Chi-restraints excluded: chain G residue 321 SER Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 293 HIS Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 321 SER Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 39 optimal weight: 0.9980 chunk 222 optimal weight: 0.0570 chunk 281 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 368 optimal weight: 0.5980 chunk 292 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 170 optimal weight: 0.4980 chunk 291 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.126675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.105901 restraints weight = 40662.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.107754 restraints weight = 32125.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.109042 restraints weight = 27295.567| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32590 Z= 0.093 Angle : 0.548 12.304 44320 Z= 0.267 Chirality : 0.039 0.138 5080 Planarity : 0.005 0.053 5620 Dihedral : 4.065 16.233 4330 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.65 % Allowed : 17.86 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 4000 helix: 0.88 (0.11), residues: 2430 sheet: None (None), residues: 0 loop : -2.27 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 7 HIS 0.004 0.001 HIS H 132 PHE 0.013 0.001 PHE G 160 TYR 0.008 0.001 TYR I 134 ARG 0.003 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 1530) hydrogen bonds : angle 3.84161 ( 4500) metal coordination : bond 0.00316 ( 80) metal coordination : angle 1.51995 ( 60) covalent geometry : bond 0.00210 (32510) covalent geometry : angle 0.54578 (44260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 373 time to evaluate : 3.710 Fit side-chains REVERT: A 242 LYS cc_start: 0.7246 (pttm) cc_final: 0.6891 (ptpt) REVERT: A 259 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7528 (tt) REVERT: A 303 MET cc_start: 0.8422 (mmm) cc_final: 0.8067 (mmt) REVERT: A 320 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: A 360 GLN cc_start: 0.7594 (pt0) cc_final: 0.6944 (pt0) REVERT: B 146 ASP cc_start: 0.8039 (t70) cc_final: 0.7610 (t70) REVERT: B 242 LYS cc_start: 0.7393 (pttm) cc_final: 0.7052 (ptpt) REVERT: B 259 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6921 (tt) REVERT: C 146 ASP cc_start: 0.8231 (t70) cc_final: 0.7828 (t0) REVERT: C 399 ILE cc_start: 0.9054 (tt) cc_final: 0.8692 (tt) REVERT: D 61 ASP cc_start: 0.7616 (m-30) cc_final: 0.7371 (m-30) REVERT: D 99 MET cc_start: 0.8469 (mmm) cc_final: 0.8138 (mmm) REVERT: D 146 ASP cc_start: 0.8378 (t70) cc_final: 0.8071 (t0) REVERT: D 399 ILE cc_start: 0.9052 (tt) cc_final: 0.8737 (tt) REVERT: E 146 ASP cc_start: 0.8236 (t70) cc_final: 0.7788 (t0) REVERT: E 242 LYS cc_start: 0.7477 (pttm) cc_final: 0.6977 (ptpt) REVERT: E 259 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7029 (tt) REVERT: E 320 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: E 358 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7884 (mttm) REVERT: E 399 ILE cc_start: 0.8946 (tt) cc_final: 0.8602 (tt) REVERT: F 61 ASP cc_start: 0.7843 (m-30) cc_final: 0.7613 (m-30) REVERT: F 399 ILE cc_start: 0.9054 (tt) cc_final: 0.8692 (tt) REVERT: G 61 ASP cc_start: 0.7613 (m-30) cc_final: 0.7376 (m-30) REVERT: G 399 ILE cc_start: 0.9053 (tt) cc_final: 0.8743 (tt) REVERT: H 146 ASP cc_start: 0.8242 (t70) cc_final: 0.7760 (t0) REVERT: H 242 LYS cc_start: 0.7467 (pttm) cc_final: 0.6973 (ptpt) REVERT: H 259 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7235 (tt) REVERT: H 320 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: H 358 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7880 (mttm) REVERT: H 399 ILE cc_start: 0.8943 (tt) cc_final: 0.8604 (tt) REVERT: I 61 ASP cc_start: 0.7620 (m-30) cc_final: 0.7371 (m-30) REVERT: I 259 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7493 (tt) REVERT: I 303 MET cc_start: 0.8421 (mmm) cc_final: 0.8067 (mmt) REVERT: I 320 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: J 146 ASP cc_start: 0.8022 (t70) cc_final: 0.7628 (t70) REVERT: J 242 LYS cc_start: 0.7395 (pttm) cc_final: 0.7067 (ptpt) REVERT: J 259 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7004 (tt) REVERT: J 320 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8110 (mt-10) outliers start: 58 outliers final: 42 residues processed: 412 average time/residue: 0.3575 time to fit residues: 256.7626 Evaluate side-chains 421 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 368 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 308 HIS Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 293 HIS Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 40 optimal weight: 7.9990 chunk 391 optimal weight: 2.9990 chunk 375 optimal weight: 0.7980 chunk 291 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 212 optimal weight: 0.4980 chunk 274 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.126973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.106967 restraints weight = 40474.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.108663 restraints weight = 32572.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.109547 restraints weight = 28005.270| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32590 Z= 0.101 Angle : 0.547 12.150 44320 Z= 0.265 Chirality : 0.039 0.134 5080 Planarity : 0.004 0.053 5620 Dihedral : 3.954 15.527 4330 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.54 % Allowed : 18.18 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 4000 helix: 1.01 (0.11), residues: 2440 sheet: None (None), residues: 0 loop : -2.11 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 7 HIS 0.003 0.001 HIS H 132 PHE 0.012 0.001 PHE G 160 TYR 0.009 0.001 TYR I 134 ARG 0.002 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 1530) hydrogen bonds : angle 3.78798 ( 4500) metal coordination : bond 0.00337 ( 80) metal coordination : angle 1.74260 ( 60) covalent geometry : bond 0.00237 (32510) covalent geometry : angle 0.54341 (44260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 385 time to evaluate : 3.419 Fit side-chains REVERT: A 242 LYS cc_start: 0.7328 (pttm) cc_final: 0.6968 (ptpt) REVERT: A 259 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7363 (tt) REVERT: A 320 GLU cc_start: 0.8289 (mp0) cc_final: 0.7960 (mp0) REVERT: A 360 GLN cc_start: 0.7540 (pt0) cc_final: 0.6846 (pt0) REVERT: B 146 ASP cc_start: 0.8113 (t70) cc_final: 0.7651 (t70) REVERT: B 242 LYS cc_start: 0.7410 (pttm) cc_final: 0.7097 (ptpt) REVERT: B 259 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6941 (tt) REVERT: C 146 ASP cc_start: 0.8260 (t70) cc_final: 0.7807 (t0) REVERT: C 399 ILE cc_start: 0.9054 (tt) cc_final: 0.8704 (tt) REVERT: D 61 ASP cc_start: 0.7632 (m-30) cc_final: 0.7383 (m-30) REVERT: D 99 MET cc_start: 0.8481 (mmm) cc_final: 0.8171 (mmm) REVERT: E 21 LEU cc_start: 0.8307 (mm) cc_final: 0.8085 (mm) REVERT: E 61 ASP cc_start: 0.7612 (m-30) cc_final: 0.7395 (m-30) REVERT: E 146 ASP cc_start: 0.8251 (t70) cc_final: 0.7741 (t0) REVERT: E 242 LYS cc_start: 0.7457 (pttm) cc_final: 0.6978 (ptpt) REVERT: E 259 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7096 (tt) REVERT: E 320 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: E 399 ILE cc_start: 0.8956 (tt) cc_final: 0.8621 (tt) REVERT: F 146 ASP cc_start: 0.8365 (t70) cc_final: 0.8078 (t0) REVERT: F 399 ILE cc_start: 0.9056 (tt) cc_final: 0.8701 (tt) REVERT: G 61 ASP cc_start: 0.7635 (m-30) cc_final: 0.7383 (m-30) REVERT: G 99 MET cc_start: 0.8440 (mmm) cc_final: 0.8107 (mmm) REVERT: H 21 LEU cc_start: 0.8306 (mm) cc_final: 0.8089 (mm) REVERT: H 146 ASP cc_start: 0.8194 (t70) cc_final: 0.7666 (t0) REVERT: H 242 LYS cc_start: 0.7446 (pttm) cc_final: 0.6971 (ptpt) REVERT: H 259 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7148 (tt) REVERT: H 320 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: H 358 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7863 (mttm) REVERT: H 399 ILE cc_start: 0.8953 (tt) cc_final: 0.8615 (tt) REVERT: I 320 GLU cc_start: 0.8299 (mp0) cc_final: 0.8087 (mp0) REVERT: J 146 ASP cc_start: 0.8121 (t70) cc_final: 0.7615 (t70) REVERT: J 242 LYS cc_start: 0.7366 (pttm) cc_final: 0.7043 (ptpt) REVERT: J 320 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: J 358 LYS cc_start: 0.8394 (mptt) cc_final: 0.7918 (ttpp) outliers start: 54 outliers final: 46 residues processed: 419 average time/residue: 0.3684 time to fit residues: 265.3504 Evaluate side-chains 420 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 367 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 308 HIS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 308 HIS Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 293 HIS Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 320 GLU Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 119 optimal weight: 0.7980 chunk 295 optimal weight: 0.9990 chunk 266 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 335 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 221 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.129037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.109762 restraints weight = 40298.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.111329 restraints weight = 32883.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.112482 restraints weight = 28506.390| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32590 Z= 0.096 Angle : 0.550 11.986 44320 Z= 0.263 Chirality : 0.039 0.140 5080 Planarity : 0.004 0.053 5620 Dihedral : 3.889 15.967 4330 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.45 % Allowed : 18.38 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 4000 helix: 1.13 (0.11), residues: 2440 sheet: None (None), residues: 0 loop : -2.07 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 7 HIS 0.003 0.001 HIS D 132 PHE 0.012 0.001 PHE G 160 TYR 0.008 0.001 TYR I 134 ARG 0.003 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 1530) hydrogen bonds : angle 3.74742 ( 4500) metal coordination : bond 0.00311 ( 80) metal coordination : angle 1.56476 ( 60) covalent geometry : bond 0.00222 (32510) covalent geometry : angle 0.54741 (44260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 379 time to evaluate : 3.910 Fit side-chains REVERT: A 242 LYS cc_start: 0.7337 (pttm) cc_final: 0.6966 (ptpt) REVERT: A 259 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7367 (tt) REVERT: A 320 GLU cc_start: 0.8259 (mp0) cc_final: 0.8027 (mp0) REVERT: A 360 GLN cc_start: 0.7529 (pt0) cc_final: 0.6891 (pt0) REVERT: B 146 ASP cc_start: 0.7958 (t70) cc_final: 0.7513 (t70) REVERT: B 147 MET cc_start: 0.7034 (mmm) cc_final: 0.6469 (mmm) REVERT: B 242 LYS cc_start: 0.7426 (pttm) cc_final: 0.7052 (ptpt) REVERT: C 146 ASP cc_start: 0.8163 (t70) cc_final: 0.7764 (t0) REVERT: C 303 MET cc_start: 0.8545 (mmm) cc_final: 0.8306 (mmt) REVERT: C 399 ILE cc_start: 0.9061 (tt) cc_final: 0.8692 (tt) REVERT: D 61 ASP cc_start: 0.7567 (m-30) cc_final: 0.7336 (m-30) REVERT: D 99 MET cc_start: 0.8361 (mmm) cc_final: 0.8116 (mmm) REVERT: D 146 ASP cc_start: 0.8321 (t70) cc_final: 0.8006 (t0) REVERT: E 21 LEU cc_start: 0.8268 (mm) cc_final: 0.8055 (mm) REVERT: E 61 ASP cc_start: 0.7629 (m-30) cc_final: 0.7372 (m-30) REVERT: E 146 ASP cc_start: 0.8196 (t70) cc_final: 0.7730 (t0) REVERT: E 242 LYS cc_start: 0.7410 (pttm) cc_final: 0.6903 (ptpt) REVERT: E 259 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7093 (tt) REVERT: E 320 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: E 399 ILE cc_start: 0.8954 (tt) cc_final: 0.8612 (tt) REVERT: F 303 MET cc_start: 0.8545 (mmm) cc_final: 0.8296 (mmt) REVERT: F 399 ILE cc_start: 0.9052 (tt) cc_final: 0.8693 (tt) REVERT: G 61 ASP cc_start: 0.7574 (m-30) cc_final: 0.7337 (m-30) REVERT: G 99 MET cc_start: 0.8453 (mmm) cc_final: 0.8147 (mmm) REVERT: H 21 LEU cc_start: 0.8267 (mm) cc_final: 0.8058 (mm) REVERT: H 146 ASP cc_start: 0.8140 (t70) cc_final: 0.7632 (t0) REVERT: H 242 LYS cc_start: 0.7405 (pttm) cc_final: 0.6905 (ptpt) REVERT: H 259 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7162 (tt) REVERT: H 320 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: H 399 ILE cc_start: 0.8954 (tt) cc_final: 0.8613 (tt) REVERT: J 146 ASP cc_start: 0.7965 (t70) cc_final: 0.7447 (t70) REVERT: J 242 LYS cc_start: 0.7451 (pttm) cc_final: 0.7074 (ptpt) REVERT: J 358 LYS cc_start: 0.8502 (mptt) cc_final: 0.8301 (mttm) outliers start: 51 outliers final: 45 residues processed: 413 average time/residue: 0.3585 time to fit residues: 254.3155 Evaluate side-chains 412 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 293 HIS Chi-restraints excluded: chain E residue 320 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 308 HIS Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 293 HIS Chi-restraints excluded: chain J residue 298 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 364 LEU Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 323 optimal weight: 0.9980 chunk 344 optimal weight: 0.3980 chunk 210 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 346 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 24 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.109836 restraints weight = 40433.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.111355 restraints weight = 33001.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.112511 restraints weight = 28643.669| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32590 Z= 0.093 Angle : 0.547 13.239 44320 Z= 0.261 Chirality : 0.039 0.140 5080 Planarity : 0.004 0.053 5620 Dihedral : 3.825 15.094 4330 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.67 % Rotamer: Outliers : 1.48 % Allowed : 18.63 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 4000 helix: 1.23 (0.11), residues: 2440 sheet: None (None), residues: 0 loop : -2.03 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 374 HIS 0.004 0.001 HIS G 132 PHE 0.012 0.001 PHE J 160 TYR 0.008 0.001 TYR I 134 ARG 0.002 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 1530) hydrogen bonds : angle 3.71800 ( 4500) metal coordination : bond 0.00327 ( 80) metal coordination : angle 1.57332 ( 60) covalent geometry : bond 0.00215 (32510) covalent geometry : angle 0.54435 (44260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9029.21 seconds wall clock time: 158 minutes 29.75 seconds (9509.75 seconds total)