Starting phenix.real_space_refine on Mon Aug 25 22:02:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xfa_22168/08_2025/6xfa_22168.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xfa_22168/08_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_22168/08_2025/6xfa_22168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xfa_22168/08_2025/6xfa_22168.map" model { file = "/net/cci-nas-00/data/ceres_data/6xfa_22168/08_2025/6xfa_22168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xfa_22168/08_2025/6xfa_22168.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J Time building chain proxies: 3.39, per 1000 atoms: 0.11 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: 2.68 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.04 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: 5.64 Time building geometry restraints manager: 3.58 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.530 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.120 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (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 ARG 0.001 0.000 ARG B 55 TYR 0.010 0.001 TYR B 440 PHE 0.011 0.001 PHE D 160 TRP 0.011 0.002 TRP H 91 HIS 0.003 0.001 HIS E 43 Details of bonding type rmsd covalent geometry : bond 0.00561 (32510) covalent geometry : angle 0.66261 (44260) hydrogen bonds : bond 0.13055 ( 1530) hydrogen bonds : angle 5.80801 ( 4500) metal coordination : bond 0.15706 ( 80) metal coordination : angle 17.92857 ( 60) *********************** 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 : 1.142 Fit side-chains REVERT: A 17 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7055 (mm-30) REVERT: A 298 CYS cc_start: 0.8245 (m) cc_final: 0.8011 (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: 0.8686 (tt) REVERT: C 399 ILE cc_start: 0.8677 (tt) cc_final: 0.8354 (tt) REVERT: D 399 ILE cc_start: 0.8800 (tt) cc_final: 0.8548 (tt) REVERT: E 147 MET cc_start: 0.7190 (mmm) cc_final: 0.6962 (mmm) REVERT: E 178 MET cc_start: 0.6709 (mtt) cc_final: 0.6508 (mtt) REVERT: E 399 ILE cc_start: 0.8838 (tt) cc_final: 0.8526 (tt) REVERT: F 399 ILE cc_start: 0.8686 (tt) cc_final: 0.8374 (tt) REVERT: G 399 ILE cc_start: 0.8801 (tt) cc_final: 0.8562 (tt) REVERT: H 147 MET cc_start: 0.7206 (mmm) cc_final: 0.6961 (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: 0.8504 (tt) outliers start: 20 outliers final: 0 residues processed: 502 average time/residue: 0.1721 time to fit residues: 139.5138 Evaluate side-chains 390 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 150 ASN D 65 ASN D 150 ASN E 150 ASN F 150 ASN G 150 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 ASN J 150 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.121308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.101497 restraints weight = 40989.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.102832 restraints weight = 33384.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.104064 restraints weight = 29054.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.104675 restraints weight = 26212.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.105389 restraints weight = 24478.871| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 32590 Z= 0.150 Angle : 0.612 9.655 44320 Z= 0.308 Chirality : 0.042 0.135 5080 Planarity : 0.005 0.053 5620 Dihedral : 4.634 19.039 4330 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.94 % Allowed : 11.79 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.13), residues: 4000 helix: -0.23 (0.11), residues: 2330 sheet: None (None), residues: 0 loop : -3.20 (0.13), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 467 TYR 0.013 0.001 TYR I 134 PHE 0.019 0.001 PHE A 16 TRP 0.009 0.001 TRP F 91 HIS 0.006 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00361 (32510) covalent geometry : angle 0.60364 (44260) hydrogen bonds : bond 0.04493 ( 1530) hydrogen bonds : angle 4.43276 ( 4500) metal coordination : bond 0.00591 ( 80) metal coordination : angle 2.77495 ( 60) *********************** 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 467 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 434 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7293 (tt) REVERT: A 320 GLU cc_start: 0.8440 (mp0) cc_final: 0.8224 (mp0) REVERT: A 399 ILE cc_start: 0.8856 (tt) cc_final: 0.8509 (tt) REVERT: B 128 ASP cc_start: 0.8460 (m-30) cc_final: 0.8255 (m-30) REVERT: B 146 ASP cc_start: 0.7973 (t70) cc_final: 0.7734 (t70) REVERT: B 320 GLU cc_start: 0.8475 (mp0) cc_final: 0.8095 (mt-10) REVERT: B 399 ILE cc_start: 0.8901 (tt) cc_final: 0.8598 (tt) REVERT: C 146 ASP cc_start: 0.8234 (t70) cc_final: 0.7933 (t0) REVERT: C 303 MET cc_start: 0.8592 (mmm) cc_final: 0.8315 (mmt) REVERT: C 399 ILE cc_start: 0.8829 (tt) cc_final: 0.8509 (tt) REVERT: D 360 GLN cc_start: 0.7977 (pm20) cc_final: 0.7748 (pm20) REVERT: D 399 ILE cc_start: 0.8931 (tt) cc_final: 0.8652 (tt) REVERT: E 146 ASP cc_start: 0.8350 (t70) cc_final: 0.8062 (t70) REVERT: E 147 MET cc_start: 0.7197 (mmm) cc_final: 0.6624 (mmm) REVERT: E 360 GLN cc_start: 0.7709 (pm20) cc_final: 0.7442 (pt0) REVERT: E 399 ILE cc_start: 0.8882 (tt) cc_final: 0.8535 (tt) REVERT: F 303 MET cc_start: 0.8603 (mmm) cc_final: 0.8321 (mmt) REVERT: F 399 ILE cc_start: 0.8839 (tt) cc_final: 0.8509 (tt) REVERT: G 360 GLN cc_start: 0.7968 (pm20) cc_final: 0.7757 (pm20) REVERT: G 399 ILE cc_start: 0.8937 (tt) cc_final: 0.8655 (tt) REVERT: H 146 ASP cc_start: 0.8336 (t70) cc_final: 0.8085 (t70) REVERT: H 360 GLN cc_start: 0.7602 (pm20) cc_final: 0.7347 (pt0) REVERT: H 399 ILE cc_start: 0.8881 (tt) cc_final: 0.8538 (tt) REVERT: I 320 GLU cc_start: 0.8432 (mp0) cc_final: 0.8217 (mp0) REVERT: I 360 GLN cc_start: 0.7867 (pm20) cc_final: 0.7563 (pm20) REVERT: I 399 ILE cc_start: 0.8847 (tt) cc_final: 0.8526 (tt) REVERT: J 128 ASP cc_start: 0.8475 (m-30) cc_final: 0.8249 (m-30) REVERT: J 146 ASP cc_start: 0.7975 (t70) cc_final: 0.7731 (t70) REVERT: J 259 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6985 (tt) REVERT: J 320 GLU cc_start: 0.8464 (mp0) cc_final: 0.8043 (mt-10) REVERT: J 321 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9119 (t) outliers start: 33 outliers final: 23 residues processed: 457 average time/residue: 0.1628 time to fit residues: 121.0476 Evaluate side-chains 406 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 380 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 221 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 354 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 325 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 359 optimal weight: 0.7980 chunk 322 optimal weight: 0.2980 chunk 206 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN C 15 GLN F 15 GLN G 15 GLN I 15 GLN J 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.125687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.105925 restraints weight = 40612.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.107372 restraints weight = 32749.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.108686 restraints weight = 28284.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.109421 restraints weight = 25370.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.110045 restraints weight = 23514.353| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1801 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= 0.100 Angle : 0.556 12.322 44320 Z= 0.273 Chirality : 0.040 0.150 5080 Planarity : 0.005 0.053 5620 Dihedral : 4.205 16.654 4330 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.25 % Allowed : 13.48 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.13), residues: 4000 helix: 0.27 (0.11), residues: 2400 sheet: None (None), residues: 0 loop : -2.65 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 467 TYR 0.011 0.001 TYR B 410 PHE 0.014 0.001 PHE G 160 TRP 0.010 0.001 TRP D 91 HIS 0.005 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00228 (32510) covalent geometry : angle 0.55063 (44260) hydrogen bonds : bond 0.03278 ( 1530) hydrogen bonds : angle 4.04824 ( 4500) metal coordination : bond 0.00415 ( 80) metal coordination : angle 2.22255 ( 60) *********************** 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 486 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 442 time to evaluate : 1.202 Fit side-chains REVERT: A 259 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7333 (tt) REVERT: A 320 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: A 399 ILE cc_start: 0.8886 (tt) cc_final: 0.8569 (tt) REVERT: B 128 ASP cc_start: 0.8435 (m-30) cc_final: 0.8207 (m-30) REVERT: B 146 ASP cc_start: 0.8018 (t70) cc_final: 0.7741 (t70) REVERT: B 242 LYS cc_start: 0.7636 (pttm) cc_final: 0.7264 (ptpt) REVERT: B 320 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: B 399 ILE cc_start: 0.8899 (tt) cc_final: 0.8629 (tt) REVERT: C 146 ASP cc_start: 0.8160 (t70) cc_final: 0.7805 (t0) REVERT: C 303 MET cc_start: 0.8553 (mmm) cc_final: 0.8290 (mmt) REVERT: C 399 ILE cc_start: 0.8968 (tt) cc_final: 0.8602 (tt) REVERT: D 320 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: D 360 GLN cc_start: 0.7714 (pm20) cc_final: 0.7466 (pt0) REVERT: D 399 ILE cc_start: 0.8947 (tt) cc_final: 0.8668 (tt) REVERT: E 146 ASP cc_start: 0.8373 (t70) cc_final: 0.8001 (t70) REVERT: E 147 MET cc_start: 0.6992 (mmm) cc_final: 0.6648 (mmp) REVERT: E 399 ILE cc_start: 0.8906 (tt) cc_final: 0.8596 (tt) REVERT: F 146 ASP cc_start: 0.8235 (t0) cc_final: 0.8024 (t0) REVERT: F 303 MET cc_start: 0.8532 (mmm) cc_final: 0.8264 (mmt) REVERT: F 399 ILE cc_start: 0.8967 (tt) cc_final: 0.8604 (tt) REVERT: G 320 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: G 360 GLN cc_start: 0.7712 (pm20) cc_final: 0.7460 (pt0) REVERT: G 399 ILE cc_start: 0.8948 (tt) cc_final: 0.8672 (tt) REVERT: H 146 ASP cc_start: 0.8189 (t70) cc_final: 0.7758 (t0) REVERT: H 399 ILE cc_start: 0.8906 (tt) cc_final: 0.8596 (tt) REVERT: I 320 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: I 399 ILE cc_start: 0.8879 (tt) cc_final: 0.8578 (tt) REVERT: J 128 ASP cc_start: 0.8446 (m-30) cc_final: 0.8208 (m-30) REVERT: J 146 ASP cc_start: 0.8032 (t70) cc_final: 0.7752 (t70) REVERT: J 242 LYS cc_start: 0.7589 (pttm) cc_final: 0.7245 (ptpt) REVERT: J 259 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6983 (tt) REVERT: J 320 GLU cc_start: 0.8385 (mp0) cc_final: 0.8091 (mt-10) outliers start: 44 outliers final: 30 residues processed: 470 average time/residue: 0.1526 time to fit residues: 118.8857 Evaluate side-chains 427 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 390 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 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 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 298 CYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 354 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 340 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 362 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 G 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.110901 restraints weight = 40413.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.111787 restraints weight = 35388.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.112599 restraints weight = 32072.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.113183 restraints weight = 29781.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.113509 restraints weight = 28214.258| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 32590 Z= 0.165 Angle : 0.603 11.673 44320 Z= 0.295 Chirality : 0.042 0.139 5080 Planarity : 0.005 0.054 5620 Dihedral : 4.327 17.307 4330 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.85 % Allowed : 14.99 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.13), residues: 4000 helix: 0.39 (0.11), residues: 2390 sheet: None (None), residues: 0 loop : -2.58 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 372 TYR 0.011 0.001 TYR A 134 PHE 0.012 0.001 PHE G 160 TRP 0.010 0.002 TRP F 374 HIS 0.004 0.001 HIS E 308 Details of bonding type rmsd covalent geometry : bond 0.00405 (32510) covalent geometry : angle 0.59640 (44260) hydrogen bonds : bond 0.04385 ( 1530) hydrogen bonds : angle 4.10025 ( 4500) metal coordination : bond 0.00555 ( 80) metal coordination : angle 2.52817 ( 60) *********************** 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 439 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 374 time to evaluate : 0.872 Fit side-chains REVERT: A 259 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7402 (tt) REVERT: A 364 LEU cc_start: 0.8069 (mt) cc_final: 0.7856 (mt) REVERT: A 399 ILE cc_start: 0.8990 (tt) cc_final: 0.8668 (tt) REVERT: B 146 ASP cc_start: 0.8052 (t70) cc_final: 0.7769 (t70) REVERT: B 242 LYS cc_start: 0.7481 (pttm) cc_final: 0.7179 (ptpt) REVERT: B 259 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7015 (tt) REVERT: B 320 GLU cc_start: 0.8456 (mp0) cc_final: 0.7990 (mt-10) REVERT: C 146 ASP cc_start: 0.8222 (t70) cc_final: 0.7887 (t0) REVERT: C 399 ILE cc_start: 0.9071 (tt) cc_final: 0.8729 (tt) REVERT: D 399 ILE cc_start: 0.8986 (tt) cc_final: 0.8694 (tt) REVERT: E 146 ASP cc_start: 0.8381 (t70) cc_final: 0.8030 (t0) REVERT: E 147 MET cc_start: 0.7176 (mmm) cc_final: 0.6849 (mmp) REVERT: E 242 LYS cc_start: 0.7524 (pttm) cc_final: 0.7114 (ptpt) REVERT: F 7 TRP cc_start: 0.7621 (m100) cc_final: 0.7405 (m100) REVERT: F 399 ILE cc_start: 0.9068 (tt) cc_final: 0.8723 (tt) REVERT: G 399 ILE cc_start: 0.8990 (tt) cc_final: 0.8697 (tt) REVERT: H 146 ASP cc_start: 0.8256 (t70) cc_final: 0.7846 (t0) REVERT: H 242 LYS cc_start: 0.7518 (pttm) cc_final: 0.7113 (ptpt) REVERT: I 259 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7354 (tt) REVERT: I 364 LEU cc_start: 0.7977 (mt) cc_final: 0.7761 (mt) REVERT: I 399 ILE cc_start: 0.9006 (tt) cc_final: 0.8694 (tt) REVERT: J 146 ASP cc_start: 0.8061 (t70) cc_final: 0.7778 (t70) REVERT: J 242 LYS cc_start: 0.7494 (pttm) cc_final: 0.7198 (ptpt) REVERT: J 259 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7007 (tt) REVERT: J 320 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8089 (mt-10) outliers start: 65 outliers final: 48 residues processed: 418 average time/residue: 0.1530 time to fit residues: 106.7173 Evaluate side-chains 402 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 349 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 349 ILE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain C residue 104 ILE 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 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 308 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 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 308 HIS 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 298 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 285 optimal weight: 2.9990 chunk 398 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 chunk 131 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.127511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110839 restraints weight = 40382.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.111765 restraints weight = 35143.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.112539 restraints weight = 31871.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.112909 restraints weight = 29740.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113204 restraints weight = 28350.467| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 32590 Z= 0.136 Angle : 0.576 12.084 44320 Z= 0.283 Chirality : 0.041 0.134 5080 Planarity : 0.005 0.054 5620 Dihedral : 4.273 17.310 4330 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.23 % Rotamer: Outliers : 1.74 % Allowed : 16.38 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.13), residues: 4000 helix: 0.49 (0.11), residues: 2410 sheet: None (None), residues: 0 loop : -2.42 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.010 0.001 TYR A 134 PHE 0.012 0.001 PHE G 160 TRP 0.015 0.002 TRP B 7 HIS 0.003 0.001 HIS G 308 Details of bonding type rmsd covalent geometry : bond 0.00330 (32510) covalent geometry : angle 0.57134 (44260) hydrogen bonds : bond 0.03912 ( 1530) hydrogen bonds : angle 4.00476 ( 4500) metal coordination : bond 0.00499 ( 80) metal coordination : angle 2.12086 ( 60) *********************** 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 422 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 361 time to evaluate : 1.520 Fit side-chains REVERT: A 259 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7370 (tt) REVERT: A 360 GLN cc_start: 0.7397 (pt0) cc_final: 0.6625 (pt0) REVERT: B 146 ASP cc_start: 0.8043 (t70) cc_final: 0.7716 (t70) REVERT: B 242 LYS cc_start: 0.7481 (pttm) cc_final: 0.7148 (ptpt) REVERT: B 259 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7010 (tt) REVERT: B 320 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: C 146 ASP cc_start: 0.8213 (t70) cc_final: 0.7849 (t0) REVERT: C 399 ILE cc_start: 0.9087 (tt) cc_final: 0.8728 (tt) REVERT: D 399 ILE cc_start: 0.8990 (tt) cc_final: 0.8683 (tt) REVERT: E 146 ASP cc_start: 0.8370 (t70) cc_final: 0.7988 (t0) REVERT: E 147 MET cc_start: 0.7122 (mmm) cc_final: 0.6795 (mmp) REVERT: E 242 LYS cc_start: 0.7448 (pttm) cc_final: 0.7035 (ptpt) REVERT: E 320 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: F 399 ILE cc_start: 0.9088 (tt) cc_final: 0.8728 (tt) REVERT: G 399 ILE cc_start: 0.9000 (tt) cc_final: 0.8697 (tt) REVERT: H 146 ASP cc_start: 0.8137 (t70) cc_final: 0.7720 (t0) REVERT: H 242 LYS cc_start: 0.7445 (pttm) cc_final: 0.7036 (ptpt) REVERT: H 320 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: I 259 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7465 (tt) REVERT: J 7 TRP cc_start: 0.7825 (m100) cc_final: 0.7468 (m100) REVERT: J 146 ASP cc_start: 0.8045 (t70) cc_final: 0.7720 (t70) REVERT: J 242 LYS cc_start: 0.7477 (pttm) cc_final: 0.7148 (ptpt) REVERT: J 259 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7010 (tt) REVERT: J 320 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8102 (mt-10) outliers start: 61 outliers final: 50 residues processed: 400 average time/residue: 0.1680 time to fit residues: 113.4156 Evaluate side-chains 402 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 344 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 321 SER Chi-restraints excluded: chain B residue 364 LEU 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 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 104 ILE 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 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 I residue 298 CYS 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 349 ILE Chi-restraints excluded: chain J residue 364 LEU 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 84 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 39 optimal weight: 0.0980 chunk 378 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 336 optimal weight: 0.0970 chunk 349 optimal weight: 3.9990 chunk 396 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.129169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.109904 restraints weight = 40186.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.111497 restraints weight = 32759.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112650 restraints weight = 28366.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.113355 restraints weight = 25550.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.113821 restraints weight = 23711.595| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32590 Z= 0.090 Angle : 0.527 12.088 44320 Z= 0.258 Chirality : 0.039 0.135 5080 Planarity : 0.004 0.053 5620 Dihedral : 3.950 15.627 4330 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.45 % Allowed : 17.26 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 4000 helix: 0.81 (0.11), residues: 2400 sheet: None (None), residues: 0 loop : -2.27 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 372 TYR 0.007 0.001 TYR B 410 PHE 0.012 0.001 PHE C 160 TRP 0.011 0.001 TRP B 7 HIS 0.003 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00202 (32510) covalent geometry : angle 0.52458 (44260) hydrogen bonds : bond 0.02814 ( 1530) hydrogen bonds : angle 3.81885 ( 4500) metal coordination : bond 0.00287 ( 80) metal coordination : angle 1.51340 ( 60) *********************** 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 452 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 401 time to evaluate : 1.185 Fit side-chains REVERT: A 259 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7391 (tt) REVERT: A 360 GLN cc_start: 0.7431 (pt0) cc_final: 0.6728 (pt0) REVERT: A 399 ILE cc_start: 0.9021 (tt) cc_final: 0.8680 (tt) REVERT: B 146 ASP cc_start: 0.7946 (t70) cc_final: 0.7571 (t70) REVERT: B 242 LYS cc_start: 0.7357 (pttm) cc_final: 0.7029 (ptpt) REVERT: B 320 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: C 146 ASP cc_start: 0.8103 (t70) cc_final: 0.7724 (t0) REVERT: C 303 MET cc_start: 0.8524 (mmm) cc_final: 0.8278 (mmt) REVERT: C 399 ILE cc_start: 0.9008 (tt) cc_final: 0.8620 (tt) REVERT: D 61 ASP cc_start: 0.7626 (m-30) cc_final: 0.7401 (m-30) REVERT: D 399 ILE cc_start: 0.8965 (tt) cc_final: 0.8729 (tt) REVERT: E 146 ASP cc_start: 0.8186 (t70) cc_final: 0.7776 (t0) REVERT: E 147 MET cc_start: 0.6995 (mmm) cc_final: 0.6676 (mmp) REVERT: E 242 LYS cc_start: 0.7407 (pttm) cc_final: 0.6973 (ptpt) REVERT: E 320 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: F 174 CYS cc_start: 0.6978 (t) cc_final: 0.6774 (t) REVERT: F 303 MET cc_start: 0.8527 (mmm) cc_final: 0.8280 (mmt) REVERT: F 399 ILE cc_start: 0.9006 (tt) cc_final: 0.8616 (tt) REVERT: G 61 ASP cc_start: 0.7623 (m-30) cc_final: 0.7400 (m-30) REVERT: G 399 ILE cc_start: 0.8973 (tt) cc_final: 0.8736 (tt) REVERT: H 146 ASP cc_start: 0.8058 (t70) cc_final: 0.7569 (t0) REVERT: H 242 LYS cc_start: 0.7391 (pttm) cc_final: 0.6968 (ptpt) REVERT: H 320 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: I 259 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7437 (tt) REVERT: I 399 ILE cc_start: 0.9020 (tt) cc_final: 0.8687 (tt) REVERT: J 7 TRP cc_start: 0.7789 (m100) cc_final: 0.7511 (m100) REVERT: J 146 ASP cc_start: 0.7962 (t70) cc_final: 0.7584 (t70) REVERT: J 242 LYS cc_start: 0.7395 (pttm) cc_final: 0.7075 (ptpt) REVERT: J 259 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6936 (tt) REVERT: J 358 LYS cc_start: 0.8471 (mptt) cc_final: 0.8044 (tmmt) outliers start: 51 outliers final: 42 residues processed: 433 average time/residue: 0.1542 time to fit residues: 115.2307 Evaluate side-chains 420 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 372 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 259 LEU Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 320 GLU 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 356 LEU 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 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 298 CYS 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 321 SER Chi-restraints excluded: chain J residue 359 THR 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 286 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 387 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 233 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 chunk 359 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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** G 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.114337 restraints weight = 40038.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115239 restraints weight = 34754.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.116099 restraints weight = 31535.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116387 restraints weight = 29301.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.116908 restraints weight = 28120.523| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2407 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= 0.095 Angle : 0.530 12.039 44320 Z= 0.257 Chirality : 0.039 0.147 5080 Planarity : 0.004 0.053 5620 Dihedral : 3.859 15.299 4330 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.68 % Allowed : 17.52 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.14), residues: 4000 helix: 0.95 (0.11), residues: 2400 sheet: None (None), residues: 0 loop : -2.14 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 372 TYR 0.007 0.001 TYR A 134 PHE 0.012 0.001 PHE G 160 TRP 0.015 0.001 TRP B 7 HIS 0.003 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00220 (32510) covalent geometry : angle 0.52704 (44260) hydrogen bonds : bond 0.03049 ( 1530) hydrogen bonds : angle 3.76955 ( 4500) metal coordination : bond 0.00317 ( 80) metal coordination : angle 1.69354 ( 60) *********************** 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 438 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 379 time to evaluate : 0.805 Fit side-chains REVERT: A 259 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7392 (tt) REVERT: A 360 GLN cc_start: 0.7405 (pt0) cc_final: 0.6744 (pt0) REVERT: A 399 ILE cc_start: 0.9030 (tt) cc_final: 0.8695 (tt) REVERT: B 146 ASP cc_start: 0.7944 (t70) cc_final: 0.7570 (t70) REVERT: B 242 LYS cc_start: 0.7338 (pttm) cc_final: 0.7045 (ptpt) REVERT: B 320 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: C 61 ASP cc_start: 0.7879 (m-30) cc_final: 0.7674 (m-30) REVERT: C 146 ASP cc_start: 0.8076 (t70) cc_final: 0.7684 (t0) REVERT: C 303 MET cc_start: 0.8483 (mmm) cc_final: 0.8222 (mmt) REVERT: C 399 ILE cc_start: 0.8997 (tt) cc_final: 0.8619 (tt) REVERT: D 61 ASP cc_start: 0.7584 (m-30) cc_final: 0.7362 (m-30) REVERT: E 21 LEU cc_start: 0.8242 (mm) cc_final: 0.8027 (mm) REVERT: E 146 ASP cc_start: 0.8142 (t70) cc_final: 0.7738 (t0) REVERT: E 147 MET cc_start: 0.7057 (mmm) cc_final: 0.6682 (mmp) REVERT: E 242 LYS cc_start: 0.7457 (pttm) cc_final: 0.6959 (ptpt) REVERT: E 320 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: F 303 MET cc_start: 0.8495 (mmm) cc_final: 0.8230 (mmt) REVERT: F 399 ILE cc_start: 0.8996 (tt) cc_final: 0.8617 (tt) REVERT: G 61 ASP cc_start: 0.7587 (m-30) cc_final: 0.7358 (m-30) REVERT: H 21 LEU cc_start: 0.8225 (mm) cc_final: 0.8015 (mm) REVERT: H 146 ASP cc_start: 0.8037 (t70) cc_final: 0.7507 (t0) REVERT: H 242 LYS cc_start: 0.7450 (pttm) cc_final: 0.6962 (ptpt) REVERT: H 320 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: I 259 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7434 (tt) REVERT: J 7 TRP cc_start: 0.7763 (m100) cc_final: 0.7540 (m100) REVERT: J 146 ASP cc_start: 0.7899 (t70) cc_final: 0.7496 (t70) REVERT: J 242 LYS cc_start: 0.7313 (pttm) cc_final: 0.7043 (ptpt) outliers start: 59 outliers final: 46 residues processed: 418 average time/residue: 0.1427 time to fit residues: 102.5010 Evaluate side-chains 420 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 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 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 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 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 293 HIS Chi-restraints excluded: chain H residue 320 GLU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 298 CYS 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 321 SER Chi-restraints excluded: chain J residue 349 ILE Chi-restraints excluded: chain J residue 359 THR 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 87 optimal weight: 0.8980 chunk 29 optimal weight: 0.0070 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 390 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.128777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109468 restraints weight = 40406.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.111036 restraints weight = 33016.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.111998 restraints weight = 28659.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112954 restraints weight = 25962.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.113283 restraints weight = 23985.373| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2465 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= 0.098 Angle : 0.534 11.848 44320 Z= 0.258 Chirality : 0.039 0.141 5080 Planarity : 0.004 0.053 5620 Dihedral : 3.829 15.268 4330 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.45 % Allowed : 18.09 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.14), residues: 4000 helix: 1.07 (0.11), residues: 2400 sheet: None (None), residues: 0 loop : -2.04 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 372 TYR 0.007 0.001 TYR A 134 PHE 0.012 0.001 PHE B 160 TRP 0.014 0.001 TRP B 7 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00227 (32510) covalent geometry : angle 0.53111 (44260) hydrogen bonds : bond 0.03094 ( 1530) hydrogen bonds : angle 3.74916 ( 4500) metal coordination : bond 0.00334 ( 80) metal coordination : angle 1.71402 ( 60) *********************** 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: 51 poor density : 380 time to evaluate : 1.280 Fit side-chains REVERT: A 360 GLN cc_start: 0.7433 (pt0) cc_final: 0.6755 (pt0) REVERT: B 146 ASP cc_start: 0.7913 (t70) cc_final: 0.7502 (t70) REVERT: B 242 LYS cc_start: 0.7375 (pttm) cc_final: 0.7012 (ptpt) REVERT: B 320 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: C 146 ASP cc_start: 0.8132 (t70) cc_final: 0.7700 (t0) REVERT: C 399 ILE cc_start: 0.9013 (tt) cc_final: 0.8643 (tt) REVERT: D 61 ASP cc_start: 0.7594 (m-30) cc_final: 0.7354 (m-30) REVERT: E 21 LEU cc_start: 0.8241 (mm) cc_final: 0.8031 (mm) REVERT: E 146 ASP cc_start: 0.8261 (t70) cc_final: 0.7790 (t0) REVERT: E 147 MET cc_start: 0.7069 (mmm) cc_final: 0.6692 (mmp) REVERT: E 242 LYS cc_start: 0.7461 (pttm) cc_final: 0.6969 (ptpt) REVERT: E 320 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: E 358 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7886 (mmtp) REVERT: F 146 ASP cc_start: 0.8230 (t70) cc_final: 0.7960 (t0) REVERT: F 303 MET cc_start: 0.8546 (mmm) cc_final: 0.8277 (mmt) REVERT: F 399 ILE cc_start: 0.9013 (tt) cc_final: 0.8640 (tt) REVERT: G 61 ASP cc_start: 0.7603 (m-30) cc_final: 0.7389 (m-30) REVERT: G 358 LYS cc_start: 0.8204 (pttp) cc_final: 0.8004 (mttp) REVERT: H 21 LEU cc_start: 0.8236 (mm) cc_final: 0.8028 (mm) REVERT: H 146 ASP cc_start: 0.8067 (t70) cc_final: 0.7487 (t0) REVERT: H 242 LYS cc_start: 0.7447 (pttm) cc_final: 0.6967 (ptpt) REVERT: H 320 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: H 358 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7882 (mmtp) REVERT: I 259 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7268 (tt) REVERT: J 146 ASP cc_start: 0.7912 (t70) cc_final: 0.7479 (t70) REVERT: J 242 LYS cc_start: 0.7326 (pttm) cc_final: 0.7005 (ptpt) outliers start: 51 outliers final: 45 residues processed: 414 average time/residue: 0.1574 time to fit residues: 112.4214 Evaluate side-chains 409 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 360 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 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 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 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 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain H residue 62 THR 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 298 CYS Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 360 GLN 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 321 SER 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 26 optimal weight: 4.9990 chunk 314 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 267 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 280 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.125800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.106431 restraints weight = 40530.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.107940 restraints weight = 33304.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.108939 restraints weight = 29073.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.109788 restraints weight = 26353.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.110276 restraints weight = 24532.765| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 32590 Z= 0.129 Angle : 0.572 12.032 44320 Z= 0.275 Chirality : 0.040 0.140 5080 Planarity : 0.005 0.053 5620 Dihedral : 3.965 15.942 4330 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.54 % Allowed : 18.09 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.14), residues: 4000 helix: 0.99 (0.11), residues: 2440 sheet: None (None), residues: 0 loop : -2.07 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 372 TYR 0.009 0.001 TYR F 440 PHE 0.011 0.001 PHE A 16 TRP 0.017 0.001 TRP E 7 HIS 0.003 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00313 (32510) covalent geometry : angle 0.56748 (44260) hydrogen bonds : bond 0.03713 ( 1530) hydrogen bonds : angle 3.80369 ( 4500) metal coordination : bond 0.00467 ( 80) metal coordination : angle 2.03784 ( 60) *********************** 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 416 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 362 time to evaluate : 1.009 Fit side-chains REVERT: A 259 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7468 (tt) REVERT: A 360 GLN cc_start: 0.7502 (pt0) cc_final: 0.6832 (pt0) REVERT: B 146 ASP cc_start: 0.7959 (t70) cc_final: 0.7499 (t70) REVERT: B 147 MET cc_start: 0.7065 (mmm) cc_final: 0.6501 (mmm) REVERT: B 242 LYS cc_start: 0.7390 (pttm) cc_final: 0.7022 (ptpt) REVERT: B 320 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: C 146 ASP cc_start: 0.8186 (t70) cc_final: 0.7782 (t0) REVERT: C 399 ILE cc_start: 0.9099 (tt) cc_final: 0.8737 (tt) REVERT: E 21 LEU cc_start: 0.8313 (mm) cc_final: 0.8087 (mm) REVERT: E 146 ASP cc_start: 0.8294 (t70) cc_final: 0.7831 (t0) REVERT: E 147 MET cc_start: 0.7104 (mmm) cc_final: 0.6773 (mmp) REVERT: E 242 LYS cc_start: 0.7491 (pttm) cc_final: 0.6995 (ptpt) REVERT: F 146 ASP cc_start: 0.8314 (t70) cc_final: 0.8047 (t0) REVERT: F 399 ILE cc_start: 0.9099 (tt) cc_final: 0.8742 (tt) REVERT: G 358 LYS cc_start: 0.8262 (pttp) cc_final: 0.7976 (mttp) REVERT: H 21 LEU cc_start: 0.8310 (mm) cc_final: 0.8089 (mm) REVERT: H 146 ASP cc_start: 0.8109 (t70) cc_final: 0.7539 (t0) REVERT: H 242 LYS cc_start: 0.7484 (pttm) cc_final: 0.6989 (ptpt) REVERT: I 259 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7387 (tt) REVERT: J 146 ASP cc_start: 0.7946 (t70) cc_final: 0.7491 (t70) REVERT: J 242 LYS cc_start: 0.7372 (pttm) cc_final: 0.7054 (ptpt) REVERT: J 259 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6938 (tt) outliers start: 54 outliers final: 50 residues processed: 399 average time/residue: 0.1598 time to fit residues: 110.2935 Evaluate side-chains 411 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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 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 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 356 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 293 HIS 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 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 308 HIS 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 298 CYS Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 360 GLN 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 321 SER 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 152 optimal weight: 3.9990 chunk 355 optimal weight: 0.0980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 320 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 364 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.124714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.105707 restraints weight = 40280.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.106951 restraints weight = 33781.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.108027 restraints weight = 29960.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108615 restraints weight = 27406.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.109165 restraints weight = 25738.192| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 32590 Z= 0.132 Angle : 0.580 12.118 44320 Z= 0.279 Chirality : 0.041 0.141 5080 Planarity : 0.005 0.053 5620 Dihedral : 4.047 16.308 4330 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.77 % Rotamer: Outliers : 1.68 % Allowed : 18.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.14), residues: 4000 helix: 0.99 (0.11), residues: 2440 sheet: None (None), residues: 0 loop : -2.07 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 55 TYR 0.009 0.001 TYR I 134 PHE 0.012 0.001 PHE A 16 TRP 0.017 0.001 TRP B 7 HIS 0.003 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00320 (32510) covalent geometry : angle 0.57564 (44260) hydrogen bonds : bond 0.03793 ( 1530) hydrogen bonds : angle 3.82882 ( 4500) metal coordination : bond 0.00494 ( 80) metal coordination : angle 1.96856 ( 60) ********************** 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 413 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 354 time to evaluate : 1.046 Fit side-chains REVERT: A 21 LEU cc_start: 0.8279 (mm) cc_final: 0.8072 (mm) REVERT: A 259 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7462 (tt) REVERT: A 320 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: B 146 ASP cc_start: 0.7957 (t70) cc_final: 0.7523 (t70) REVERT: B 147 MET cc_start: 0.7075 (mmm) cc_final: 0.6518 (mmm) REVERT: B 242 LYS cc_start: 0.7386 (pttm) cc_final: 0.7016 (ptpt) REVERT: B 320 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: C 146 ASP cc_start: 0.8213 (t70) cc_final: 0.7794 (t0) REVERT: C 399 ILE cc_start: 0.9092 (tt) cc_final: 0.8742 (tt) REVERT: E 146 ASP cc_start: 0.8275 (t70) cc_final: 0.7863 (t0) REVERT: E 147 MET cc_start: 0.7109 (mmm) cc_final: 0.6788 (mmp) REVERT: E 242 LYS cc_start: 0.7479 (pttm) cc_final: 0.6992 (ptpt) REVERT: E 358 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7939 (mttp) REVERT: F 146 ASP cc_start: 0.8322 (t70) cc_final: 0.8051 (t0) REVERT: F 399 ILE cc_start: 0.9099 (tt) cc_final: 0.8749 (tt) REVERT: G 358 LYS cc_start: 0.8295 (pttp) cc_final: 0.7950 (mttp) REVERT: H 146 ASP cc_start: 0.8152 (t70) cc_final: 0.7588 (t0) REVERT: H 242 LYS cc_start: 0.7467 (pttm) cc_final: 0.6985 (ptpt) REVERT: H 358 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7875 (mttm) REVERT: I 259 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7520 (tt) REVERT: J 146 ASP cc_start: 0.7968 (t70) cc_final: 0.7533 (t70) REVERT: J 242 LYS cc_start: 0.7396 (pttm) cc_final: 0.7043 (ptpt) REVERT: J 259 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6957 (tt) outliers start: 59 outliers final: 50 residues processed: 396 average time/residue: 0.1647 time to fit residues: 112.8359 Evaluate side-chains 395 residues out of total 3510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 340 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 259 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 356 LEU 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 300 LEU 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 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 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 293 HIS 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 259 LEU Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 298 CYS Chi-restraints excluded: chain G residue 356 LEU Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 308 HIS 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 298 CYS Chi-restraints excluded: chain I residue 360 GLN 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 321 SER Chi-restraints excluded: chain J residue 472 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.2057 > 50: distance: 67 - 87: 17.167 distance: 71 - 95: 15.730 distance: 77 - 102: 12.321 distance: 82 - 87: 14.660 distance: 83 - 114: 8.174 distance: 87 - 88: 14.046 distance: 88 - 89: 12.899 distance: 88 - 91: 5.652 distance: 89 - 90: 26.166 distance: 89 - 95: 25.512 distance: 90 - 122: 9.942 distance: 91 - 92: 10.222 distance: 92 - 93: 18.747 distance: 92 - 94: 16.550 distance: 95 - 96: 14.647 distance: 96 - 97: 8.689 distance: 96 - 99: 13.455 distance: 97 - 98: 6.463 distance: 97 - 102: 17.410 distance: 98 - 133: 16.210 distance: 99 - 100: 18.256 distance: 99 - 101: 20.879 distance: 102 - 103: 6.250 distance: 103 - 104: 22.959 distance: 103 - 106: 8.394 distance: 104 - 105: 15.832 distance: 104 - 114: 17.629 distance: 105 - 142: 21.092 distance: 106 - 107: 8.022 distance: 107 - 108: 7.680 distance: 107 - 109: 13.948 distance: 108 - 110: 13.177 distance: 109 - 111: 16.891 distance: 110 - 112: 11.655 distance: 111 - 112: 10.462 distance: 112 - 113: 7.504 distance: 114 - 115: 10.225 distance: 115 - 116: 9.997 distance: 115 - 118: 9.589 distance: 116 - 117: 24.992 distance: 116 - 122: 8.845 distance: 117 - 148: 39.655 distance: 118 - 119: 10.566 distance: 118 - 120: 19.633 distance: 119 - 121: 9.685 distance: 122 - 123: 9.409 distance: 123 - 124: 11.033 distance: 123 - 126: 5.399 distance: 124 - 125: 12.635 distance: 124 - 133: 11.582 distance: 125 - 155: 9.489 distance: 126 - 127: 9.720 distance: 127 - 128: 4.921 distance: 127 - 129: 6.583 distance: 128 - 130: 18.619 distance: 129 - 131: 11.004 distance: 130 - 132: 16.914 distance: 131 - 132: 15.284 distance: 133 - 134: 14.735 distance: 134 - 135: 23.312 distance: 134 - 137: 5.404 distance: 135 - 136: 32.425 distance: 135 - 142: 39.722 distance: 136 - 164: 12.759 distance: 137 - 138: 7.229 distance: 138 - 139: 9.855 distance: 139 - 140: 23.160 distance: 140 - 141: 7.403 distance: 142 - 143: 13.765 distance: 143 - 144: 25.786 distance: 143 - 146: 36.459 distance: 144 - 145: 18.298 distance: 144 - 148: 26.865 distance: 145 - 171: 27.445 distance: 146 - 147: 16.460 distance: 148 - 149: 3.687 distance: 149 - 150: 12.202 distance: 149 - 152: 9.483 distance: 150 - 151: 16.788 distance: 150 - 155: 16.461 distance: 152 - 153: 17.925 distance: 152 - 154: 23.615 distance: 156 - 157: 6.587 distance: 156 - 159: 5.479 distance: 157 - 158: 15.704 distance: 157 - 164: 11.047 distance: 159 - 160: 14.263 distance: 161 - 162: 11.748 distance: 161 - 163: 11.446 distance: 164 - 165: 10.068 distance: 165 - 166: 7.949 distance: 166 - 167: 5.506 distance: 168 - 169: 5.511 distance: 168 - 170: 10.138