Starting phenix.real_space_refine on Mon Aug 25 04:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hzx_35091/08_2025/8hzx_35091.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hzx_35091/08_2025/8hzx_35091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hzx_35091/08_2025/8hzx_35091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hzx_35091/08_2025/8hzx_35091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hzx_35091/08_2025/8hzx_35091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hzx_35091/08_2025/8hzx_35091.map" } resolution = 2.68 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= -0.001 sd= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16242 2.51 5 N 4236 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 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: 25320 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: A, B, C, D, E Time building chain proxies: 4.49, per 1000 atoms: 0.18 Number of scatterers: 25320 At special positions: 0 Unit cell: (169.338, 158.184, 94.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4734 8.00 N 4236 7.00 C 16242 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: 2.04 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 30 sheets defined 36.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 86 removed outlier: 3.661A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.589A pdb=" N LEU F 124 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.580A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.816A pdb=" N THR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.734A pdb=" N ASN F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.899A pdb=" N ALA F 284 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET F 285 " --> pdb=" O SER F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.640A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 439 through 449 removed outlier: 4.126A pdb=" N LEU F 443 " --> pdb=" O SER F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 493 Processing helix chain 'F' and resid 524 through 532 Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.661A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.589A pdb=" N LEU A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.817A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.733A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.899A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.640A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 439 through 449 removed outlier: 4.126A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 86 removed outlier: 3.661A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.589A pdb=" N LEU B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.816A pdb=" N THR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.733A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.898A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.641A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 439 through 449 removed outlier: 4.127A pdb=" N LEU B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 86 removed outlier: 3.661A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.589A pdb=" N LEU C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.817A pdb=" N THR C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.734A pdb=" N ASN C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.899A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.640A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 439 through 449 removed outlier: 4.126A pdb=" N LEU C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 86 removed outlier: 3.661A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.589A pdb=" N LEU D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.817A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.734A pdb=" N ASN D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.899A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 285 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.641A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 439 through 449 removed outlier: 4.127A pdb=" N LEU D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 493 Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 86 removed outlier: 3.661A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.589A pdb=" N LEU E 124 " --> pdb=" O PHE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.579A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 205 removed outlier: 3.815A pdb=" N THR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.734A pdb=" N ASN E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 3.900A pdb=" N ALA E 284 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET E 285 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.640A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 439 through 449 removed outlier: 4.126A pdb=" N LEU E 443 " --> pdb=" O SER E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 524 through 532 Processing sheet with id=AA1, first strand: chain 'F' and resid 37 through 40 removed outlier: 3.541A pdb=" N GLN F 243 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER F 266 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER F 328 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS F 353 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR F 65 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU F 115 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA F 67 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS F 117 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET F 69 " --> pdb=" O HIS F 117 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.390A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE F 431 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 438 " --> pdb=" O ILE F 431 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL F 458 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 471 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY F 460 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL F 469 " --> pdb=" O GLY F 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY F 467 " --> pdb=" O PRO F 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.541A pdb=" N GLN A 243 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 266 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 328 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 353 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.704A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A 65 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU A 115 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 67 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N HIS A 117 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET A 69 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.391A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE A 431 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 438 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 458 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 460 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL A 469 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY A 467 " --> pdb=" O PRO A 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.541A pdb=" N GLN B 243 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 266 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 328 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 353 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR B 65 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU B 115 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA B 67 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS B 117 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET B 69 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.390A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE B 431 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 438 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 458 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY B 460 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL B 469 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY B 467 " --> pdb=" O PRO B 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.542A pdb=" N GLN C 243 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER C 266 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 328 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 353 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C 65 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU C 115 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA C 67 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS C 117 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N MET C 69 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.390A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE C 431 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 438 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL C 458 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 471 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY C 460 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL C 469 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 467 " --> pdb=" O PRO C 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.541A pdb=" N GLN D 243 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER D 266 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 328 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 353 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR D 65 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU D 115 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA D 67 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS D 117 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET D 69 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.389A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.817A pdb=" N ILE D 431 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 438 " --> pdb=" O ILE D 431 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL D 458 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU D 471 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY D 460 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL D 469 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY D 467 " --> pdb=" O PRO D 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 37 through 40 removed outlier: 3.541A pdb=" N GLN E 243 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER E 266 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 328 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS E 353 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.705A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR E 65 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU E 115 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA E 67 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS E 117 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET E 69 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.390A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 431 through 433 removed outlier: 3.818A pdb=" N ILE E 431 " --> pdb=" O VAL E 438 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL E 438 " --> pdb=" O ILE E 431 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 453 through 463 removed outlier: 6.475A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL E 458 " --> pdb=" O LEU E 471 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 471 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY E 460 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL E 469 " --> pdb=" O GLY E 460 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY E 467 " --> pdb=" O PRO E 462 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2502 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: 5.86 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4278 1.30 - 1.42: 6444 1.42 - 1.55: 14973 1.55 - 1.68: 3 1.68 - 1.80: 192 Bond restraints: 25890 Sorted by residual: bond pdb=" CA TYR E 174 " pdb=" C TYR E 174 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.22e-02 6.72e+03 3.55e+01 bond pdb=" CA TYR C 174 " pdb=" C TYR C 174 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.22e-02 6.72e+03 3.47e+01 bond pdb=" CA TYR A 174 " pdb=" C TYR A 174 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.22e-02 6.72e+03 3.47e+01 bond pdb=" CA TYR D 174 " pdb=" C TYR D 174 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.22e-02 6.72e+03 3.46e+01 bond pdb=" CA TYR F 174 " pdb=" C TYR F 174 " ideal model delta sigma weight residual 1.522 1.450 0.072 1.22e-02 6.72e+03 3.44e+01 ... (remaining 25885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 34349 2.31 - 4.61: 677 4.61 - 6.92: 74 6.92 - 9.23: 6 9.23 - 11.53: 12 Bond angle restraints: 35118 Sorted by residual: angle pdb=" N VAL D 253 " pdb=" CA VAL D 253 " pdb=" C VAL D 253 " ideal model delta sigma weight residual 111.90 100.37 11.53 8.10e-01 1.52e+00 2.03e+02 angle pdb=" N VAL E 253 " pdb=" CA VAL E 253 " pdb=" C VAL E 253 " ideal model delta sigma weight residual 111.90 100.38 11.52 8.10e-01 1.52e+00 2.02e+02 angle pdb=" N VAL C 253 " pdb=" CA VAL C 253 " pdb=" C VAL C 253 " ideal model delta sigma weight residual 111.90 100.38 11.52 8.10e-01 1.52e+00 2.02e+02 angle pdb=" N VAL F 253 " pdb=" CA VAL F 253 " pdb=" C VAL F 253 " ideal model delta sigma weight residual 111.90 100.39 11.51 8.10e-01 1.52e+00 2.02e+02 angle pdb=" N VAL B 253 " pdb=" CA VAL B 253 " pdb=" C VAL B 253 " ideal model delta sigma weight residual 111.90 100.43 11.47 8.10e-01 1.52e+00 2.01e+02 ... (remaining 35113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 13728 17.59 - 35.18: 1332 35.18 - 52.77: 378 52.77 - 70.36: 48 70.36 - 87.95: 36 Dihedral angle restraints: 15522 sinusoidal: 6252 harmonic: 9270 Sorted by residual: dihedral pdb=" CA ALA C 504 " pdb=" C ALA C 504 " pdb=" N LEU C 505 " pdb=" CA LEU C 505 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ALA E 504 " pdb=" C ALA E 504 " pdb=" N LEU E 505 " pdb=" CA LEU E 505 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ALA F 504 " pdb=" C ALA F 504 " pdb=" N LEU F 505 " pdb=" CA LEU F 505 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 15519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3295 0.071 - 0.142: 579 0.142 - 0.214: 74 0.214 - 0.285: 24 0.285 - 0.356: 6 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CB VAL C 363 " pdb=" CA VAL C 363 " pdb=" CG1 VAL C 363 " pdb=" CG2 VAL C 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL D 363 " pdb=" CA VAL D 363 " pdb=" CG1 VAL D 363 " pdb=" CG2 VAL D 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB VAL A 363 " pdb=" CA VAL A 363 " pdb=" CG1 VAL A 363 " pdb=" CG2 VAL A 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 3975 not shown) Planarity restraints: 4476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 362 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C ILE B 362 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE B 362 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 363 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 362 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C ILE D 362 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE D 362 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL D 363 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 362 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C ILE A 362 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE A 362 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL A 363 " 0.016 2.00e-02 2.50e+03 ... (remaining 4473 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 408 2.67 - 3.22: 23275 3.22 - 3.78: 38556 3.78 - 4.34: 56368 4.34 - 4.90: 91572 Nonbonded interactions: 210179 Sorted by model distance: nonbonded pdb=" OD2 ASP D 72 " pdb=" OH TYR D 249 " model vdw 2.107 3.040 nonbonded pdb=" OD2 ASP C 72 " pdb=" OH TYR C 249 " model vdw 2.108 3.040 nonbonded pdb=" OD2 ASP A 72 " pdb=" OH TYR A 249 " model vdw 2.108 3.040 nonbonded pdb=" OD2 ASP F 72 " pdb=" OH TYR F 249 " model vdw 2.108 3.040 nonbonded pdb=" OD2 ASP E 72 " pdb=" OH TYR E 249 " model vdw 2.108 3.040 ... (remaining 210174 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 'F' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.590 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.006 0.073 25890 Z= 0.414 Angle : 0.768 11.532 35118 Z= 0.492 Chirality : 0.058 0.356 3978 Planarity : 0.005 0.029 4476 Dihedral : 15.723 87.951 9558 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.44 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.14), residues: 3168 helix: 0.05 (0.16), residues: 1086 sheet: -0.84 (0.21), residues: 582 loop : -1.24 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 150 TYR 0.016 0.002 TYR D 174 PHE 0.010 0.002 PHE E 315 TRP 0.009 0.002 TRP E 230 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00644 (25890) covalent geometry : angle 0.76841 (35118) hydrogen bonds : bond 0.18709 ( 876) hydrogen bonds : angle 7.16466 ( 2502) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.029 Fit side-chains REVERT: F 150 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7619 (mtm-85) REVERT: F 154 GLN cc_start: 0.8082 (mm110) cc_final: 0.7654 (mt0) REVERT: F 163 ASP cc_start: 0.8310 (t70) cc_final: 0.8042 (t70) REVERT: F 281 LYS cc_start: 0.7465 (tttm) cc_final: 0.7163 (ptmt) REVERT: F 320 MET cc_start: 0.7417 (ppp) cc_final: 0.6900 (ppp) REVERT: F 399 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8310 (mttp) REVERT: A 154 GLN cc_start: 0.7974 (mm110) cc_final: 0.7676 (mt0) REVERT: A 320 MET cc_start: 0.7346 (ppp) cc_final: 0.6998 (ppp) REVERT: B 154 GLN cc_start: 0.8133 (mm110) cc_final: 0.7670 (mt0) REVERT: C 150 ARG cc_start: 0.7803 (mmt90) cc_final: 0.7525 (mtm-85) REVERT: C 154 GLN cc_start: 0.8037 (mm110) cc_final: 0.7711 (mt0) REVERT: C 163 ASP cc_start: 0.8252 (t70) cc_final: 0.7960 (t70) REVERT: C 281 LYS cc_start: 0.7655 (tttm) cc_final: 0.7276 (ptmt) REVERT: C 428 LYS cc_start: 0.8611 (mttm) cc_final: 0.8369 (mptt) REVERT: D 85 MET cc_start: 0.8961 (mtt) cc_final: 0.8471 (mtt) REVERT: D 154 GLN cc_start: 0.8093 (mm110) cc_final: 0.7741 (mt0) REVERT: D 197 MET cc_start: 0.8688 (mmp) cc_final: 0.8364 (mmm) REVERT: E 85 MET cc_start: 0.8946 (mtt) cc_final: 0.8552 (mtt) REVERT: E 154 GLN cc_start: 0.8182 (mm110) cc_final: 0.7854 (mt0) REVERT: E 197 MET cc_start: 0.8603 (mmp) cc_final: 0.8303 (mmm) REVERT: E 320 MET cc_start: 0.7220 (ppp) cc_final: 0.6721 (ppp) REVERT: E 416 ASP cc_start: 0.7734 (t0) cc_final: 0.7530 (t0) REVERT: E 428 LYS cc_start: 0.8498 (mttm) cc_final: 0.8246 (mmtt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.8553 time to fit residues: 202.0744 Evaluate side-chains 166 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 ASN F 108 HIS F 160 ASN F 243 GLN A 108 HIS A 160 ASN A 243 GLN B 39 HIS B 108 HIS B 160 ASN B 243 GLN C 17 ASN C 108 HIS C 160 ASN C 243 GLN D 39 HIS D 108 HIS D 160 ASN D 243 GLN E 39 HIS E 108 HIS E 160 ASN E 243 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.153873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101068 restraints weight = 30361.113| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.96 r_work: 0.3078 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 25890 Z= 0.305 Angle : 0.722 7.004 35118 Z= 0.387 Chirality : 0.054 0.222 3978 Planarity : 0.005 0.049 4476 Dihedral : 5.667 25.822 3426 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.60 % Favored : 93.12 % Rotamer: Outliers : 3.83 % Allowed : 12.44 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.05 (0.15), residues: 3168 helix: 0.19 (0.16), residues: 1086 sheet: -0.78 (0.19), residues: 654 loop : -1.28 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 529 TYR 0.014 0.003 TYR C 218 PHE 0.016 0.002 PHE C 120 TRP 0.013 0.003 TRP F 230 HIS 0.009 0.002 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00748 (25890) covalent geometry : angle 0.72151 (35118) hydrogen bonds : bond 0.06071 ( 876) hydrogen bonds : angle 5.33666 ( 2502) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 172 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7979 (mm110) cc_final: 0.7573 (mt0) REVERT: F 163 ASP cc_start: 0.8454 (t70) cc_final: 0.8188 (t70) REVERT: F 281 LYS cc_start: 0.7431 (tttm) cc_final: 0.7032 (ptmt) REVERT: F 320 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7040 (ppp) REVERT: A 154 GLN cc_start: 0.7909 (mm110) cc_final: 0.7463 (mt0) REVERT: A 320 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7169 (ppp) REVERT: B 154 GLN cc_start: 0.8058 (mm110) cc_final: 0.7595 (mt0) REVERT: B 320 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6274 (ppp) REVERT: B 373 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7620 (p0) REVERT: C 58 MET cc_start: 0.8443 (mtm) cc_final: 0.8135 (mtt) REVERT: C 150 ARG cc_start: 0.8329 (mmt90) cc_final: 0.8064 (mmt90) REVERT: C 154 GLN cc_start: 0.7991 (mm110) cc_final: 0.7616 (mt0) REVERT: C 163 ASP cc_start: 0.8373 (t70) cc_final: 0.8102 (t70) REVERT: C 347 TYR cc_start: 0.8599 (m-80) cc_final: 0.8361 (m-80) REVERT: D 85 MET cc_start: 0.8929 (mtt) cc_final: 0.8633 (mtt) REVERT: D 154 GLN cc_start: 0.8135 (mm110) cc_final: 0.7726 (mt0) REVERT: D 373 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7415 (p0) REVERT: E 85 MET cc_start: 0.8917 (mtt) cc_final: 0.8620 (mtt) REVERT: E 154 GLN cc_start: 0.8168 (mm110) cc_final: 0.7735 (mt0) REVERT: E 281 LYS cc_start: 0.7741 (ptmt) cc_final: 0.7428 (ptmm) REVERT: E 373 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7506 (p0) REVERT: E 416 ASP cc_start: 0.7852 (t0) cc_final: 0.7591 (t0) REVERT: E 418 GLU cc_start: 0.6971 (tt0) cc_final: 0.6771 (mt-10) REVERT: E 428 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8337 (mmtt) outliers start: 106 outliers final: 50 residues processed: 255 average time/residue: 0.7016 time to fit residues: 205.9434 Evaluate side-chains 219 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 316 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 286 optimal weight: 0.4980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102007 restraints weight = 30216.598| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.94 r_work: 0.3073 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25890 Z= 0.179 Angle : 0.598 7.055 35118 Z= 0.320 Chirality : 0.048 0.196 3978 Planarity : 0.004 0.036 4476 Dihedral : 5.396 27.851 3426 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 3.29 % Allowed : 14.03 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.84 (0.15), residues: 3168 helix: 0.54 (0.16), residues: 1086 sheet: -0.77 (0.19), residues: 666 loop : -1.26 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 130 TYR 0.009 0.001 TYR F 148 PHE 0.009 0.001 PHE E 225 TRP 0.007 0.002 TRP D 402 HIS 0.007 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00432 (25890) covalent geometry : angle 0.59775 (35118) hydrogen bonds : bond 0.04786 ( 876) hydrogen bonds : angle 4.93553 ( 2502) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 165 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: F 150 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6880 (mpt-90) REVERT: F 154 GLN cc_start: 0.7891 (mm110) cc_final: 0.7522 (mt0) REVERT: F 163 ASP cc_start: 0.8419 (t70) cc_final: 0.8169 (t70) REVERT: F 281 LYS cc_start: 0.7405 (tttm) cc_final: 0.6982 (ptmt) REVERT: F 320 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6823 (ppp) REVERT: F 428 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8117 (mttm) REVERT: A 154 GLN cc_start: 0.7882 (mm110) cc_final: 0.7457 (mt0) REVERT: A 320 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7038 (ppp) REVERT: A 337 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8275 (mm) REVERT: B 154 GLN cc_start: 0.7986 (mm110) cc_final: 0.7560 (mt0) REVERT: B 320 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6218 (ppp) REVERT: B 337 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8315 (mm) REVERT: B 373 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7589 (p0) REVERT: B 425 ASP cc_start: 0.8217 (t0) cc_final: 0.7907 (t70) REVERT: C 150 ARG cc_start: 0.8325 (mmt90) cc_final: 0.8047 (mmt90) REVERT: C 154 GLN cc_start: 0.7965 (mm110) cc_final: 0.7566 (mt0) REVERT: C 163 ASP cc_start: 0.8381 (t70) cc_final: 0.8128 (t70) REVERT: C 281 LYS cc_start: 0.7361 (tttm) cc_final: 0.6958 (ptmt) REVERT: D 85 MET cc_start: 0.8944 (mtt) cc_final: 0.8563 (mtt) REVERT: D 150 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7527 (mpt-90) REVERT: D 154 GLN cc_start: 0.8026 (mm110) cc_final: 0.7690 (mt0) REVERT: D 322 GLU cc_start: 0.8419 (mp0) cc_final: 0.7937 (mp0) REVERT: D 373 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7376 (p0) REVERT: E 85 MET cc_start: 0.8916 (mtt) cc_final: 0.8540 (mtt) REVERT: E 150 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7356 (mpt-90) REVERT: E 154 GLN cc_start: 0.8079 (mm110) cc_final: 0.7656 (mt0) REVERT: E 373 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7433 (p0) REVERT: E 416 ASP cc_start: 0.7767 (t0) cc_final: 0.7488 (t0) REVERT: E 428 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8336 (mmtt) outliers start: 91 outliers final: 46 residues processed: 238 average time/residue: 0.6989 time to fit residues: 191.4934 Evaluate side-chains 219 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 428 LYS Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 170 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104589 restraints weight = 30233.336| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.91 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25890 Z= 0.139 Angle : 0.564 7.765 35118 Z= 0.299 Chirality : 0.046 0.183 3978 Planarity : 0.004 0.035 4476 Dihedral : 5.186 29.012 3426 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.41 % Favored : 93.40 % Rotamer: Outliers : 3.07 % Allowed : 14.90 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.60 (0.15), residues: 3168 helix: 0.89 (0.16), residues: 1086 sheet: -0.65 (0.19), residues: 666 loop : -1.26 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 130 TYR 0.010 0.001 TYR E 318 PHE 0.009 0.001 PHE E 225 TRP 0.007 0.001 TRP F 230 HIS 0.007 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00327 (25890) covalent geometry : angle 0.56425 (35118) hydrogen bonds : bond 0.04159 ( 876) hydrogen bonds : angle 4.68968 ( 2502) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 171 time to evaluate : 1.214 Fit side-chains REVERT: F 154 GLN cc_start: 0.7935 (mm110) cc_final: 0.7569 (mt0) REVERT: F 163 ASP cc_start: 0.8433 (t70) cc_final: 0.8164 (t70) REVERT: F 281 LYS cc_start: 0.7390 (tttm) cc_final: 0.6980 (ptmt) REVERT: A 154 GLN cc_start: 0.7877 (mm110) cc_final: 0.7515 (mt0) REVERT: A 260 GLN cc_start: 0.8138 (tt0) cc_final: 0.7897 (tt0) REVERT: A 320 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.7079 (ppp) REVERT: A 337 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8303 (mm) REVERT: B 154 GLN cc_start: 0.7900 (mm110) cc_final: 0.7506 (mt0) REVERT: B 260 GLN cc_start: 0.8054 (tt0) cc_final: 0.7797 (tt0) REVERT: B 320 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7049 (ppp) REVERT: B 337 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 425 ASP cc_start: 0.8086 (t0) cc_final: 0.7877 (t70) REVERT: C 154 GLN cc_start: 0.7890 (mm110) cc_final: 0.7513 (mt0) REVERT: C 163 ASP cc_start: 0.8389 (t70) cc_final: 0.8118 (t70) REVERT: C 281 LYS cc_start: 0.7328 (tttm) cc_final: 0.6931 (ptmt) REVERT: C 322 GLU cc_start: 0.8379 (mp0) cc_final: 0.8028 (mp0) REVERT: D 85 MET cc_start: 0.8924 (mtt) cc_final: 0.8497 (mtt) REVERT: D 154 GLN cc_start: 0.7951 (mm110) cc_final: 0.7696 (mt0) REVERT: D 373 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7343 (p0) REVERT: E 85 MET cc_start: 0.8941 (mtt) cc_final: 0.8594 (mtt) REVERT: E 154 GLN cc_start: 0.8008 (mm110) cc_final: 0.7694 (mt0) REVERT: E 320 MET cc_start: 0.7088 (ppp) cc_final: 0.6507 (pmm) REVERT: E 322 GLU cc_start: 0.8371 (mp0) cc_final: 0.8047 (mp0) REVERT: E 373 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7415 (p0) REVERT: E 416 ASP cc_start: 0.7691 (t70) cc_final: 0.7398 (t0) outliers start: 85 outliers final: 44 residues processed: 238 average time/residue: 0.6722 time to fit residues: 185.4369 Evaluate side-chains 213 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 438 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 263 optimal weight: 0.9990 chunk 294 optimal weight: 5.9990 chunk 144 optimal weight: 0.0050 chunk 289 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 285 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 253 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.161313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111866 restraints weight = 30751.872| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.90 r_work: 0.3224 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25890 Z= 0.103 Angle : 0.524 10.521 35118 Z= 0.272 Chirality : 0.045 0.155 3978 Planarity : 0.004 0.032 4476 Dihedral : 4.920 30.653 3426 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.91 % Rotamer: Outliers : 2.57 % Allowed : 15.87 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.15), residues: 3168 helix: 1.16 (0.17), residues: 1086 sheet: -0.59 (0.20), residues: 648 loop : -1.11 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.010 0.001 TYR D 318 PHE 0.008 0.001 PHE C 225 TRP 0.009 0.001 TRP A 290 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00232 (25890) covalent geometry : angle 0.52364 (35118) hydrogen bonds : bond 0.03503 ( 876) hydrogen bonds : angle 4.44485 ( 2502) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: F 150 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6998 (mpt-90) REVERT: F 154 GLN cc_start: 0.7888 (mm110) cc_final: 0.7538 (mt0) REVERT: F 163 ASP cc_start: 0.8410 (t70) cc_final: 0.8152 (t70) REVERT: F 281 LYS cc_start: 0.7446 (tttm) cc_final: 0.7029 (ptmt) REVERT: F 322 GLU cc_start: 0.8384 (mp0) cc_final: 0.8182 (mp0) REVERT: F 416 ASP cc_start: 0.7591 (t70) cc_final: 0.7334 (t70) REVERT: A 154 GLN cc_start: 0.7705 (mm110) cc_final: 0.7369 (mt0) REVERT: A 260 GLN cc_start: 0.8078 (tt0) cc_final: 0.7834 (tt0) REVERT: A 320 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6737 (ppp) REVERT: B 154 GLN cc_start: 0.7782 (mm110) cc_final: 0.7426 (mt0) REVERT: B 260 GLN cc_start: 0.8011 (tt0) cc_final: 0.7763 (tt0) REVERT: B 425 ASP cc_start: 0.8061 (t0) cc_final: 0.7858 (t0) REVERT: C 92 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8396 (mpp) REVERT: C 154 GLN cc_start: 0.7857 (mm110) cc_final: 0.7526 (mt0) REVERT: C 281 LYS cc_start: 0.7311 (tttm) cc_final: 0.6916 (ptmt) REVERT: C 335 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: D 150 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7787 (mpt-90) REVERT: D 154 GLN cc_start: 0.7884 (mm110) cc_final: 0.7650 (mt0) REVERT: D 373 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7289 (p0) REVERT: E 150 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7410 (mpt-90) REVERT: E 154 GLN cc_start: 0.7923 (mm110) cc_final: 0.7613 (mt0) REVERT: E 416 ASP cc_start: 0.7663 (t70) cc_final: 0.7384 (t0) REVERT: E 428 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8430 (mmtt) outliers start: 71 outliers final: 39 residues processed: 230 average time/residue: 0.7422 time to fit residues: 196.5856 Evaluate side-chains 207 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 208 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 257 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 314 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.158428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108623 restraints weight = 30850.998| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.89 r_work: 0.3169 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25890 Z= 0.167 Angle : 0.584 9.024 35118 Z= 0.307 Chirality : 0.047 0.187 3978 Planarity : 0.004 0.034 4476 Dihedral : 5.117 29.868 3426 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.50 % Favored : 93.31 % Rotamer: Outliers : 2.78 % Allowed : 16.34 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.44 (0.15), residues: 3168 helix: 1.09 (0.16), residues: 1080 sheet: -0.55 (0.19), residues: 666 loop : -1.23 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.012 0.001 TYR E 318 PHE 0.012 0.001 PHE D 225 TRP 0.007 0.002 TRP F 230 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00404 (25890) covalent geometry : angle 0.58354 (35118) hydrogen bonds : bond 0.04356 ( 876) hydrogen bonds : angle 4.63302 ( 2502) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 164 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: F 150 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.6832 (mpt-90) REVERT: F 154 GLN cc_start: 0.7993 (mm110) cc_final: 0.7672 (mt0) REVERT: F 163 ASP cc_start: 0.8438 (t70) cc_final: 0.8174 (t70) REVERT: F 320 MET cc_start: 0.6989 (ppp) cc_final: 0.6773 (ppp) REVERT: A 154 GLN cc_start: 0.7766 (mm110) cc_final: 0.7442 (mt0) REVERT: A 320 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.7114 (ppp) REVERT: A 337 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8271 (mm) REVERT: B 154 GLN cc_start: 0.7820 (mm110) cc_final: 0.7546 (mt0) REVERT: B 260 GLN cc_start: 0.8067 (tt0) cc_final: 0.7822 (tt0) REVERT: B 322 GLU cc_start: 0.8555 (mp0) cc_final: 0.8248 (mp0) REVERT: B 335 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: B 337 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 425 ASP cc_start: 0.8100 (t0) cc_final: 0.7860 (t0) REVERT: C 154 GLN cc_start: 0.7961 (mm110) cc_final: 0.7637 (mt0) REVERT: C 163 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8050 (t70) REVERT: C 281 LYS cc_start: 0.7360 (tttm) cc_final: 0.6936 (ptmt) REVERT: D 150 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7553 (mpt-90) REVERT: D 154 GLN cc_start: 0.7911 (mm110) cc_final: 0.7649 (mt0) REVERT: D 373 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7296 (p0) REVERT: E 150 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7381 (mpt-90) REVERT: E 154 GLN cc_start: 0.7970 (mm110) cc_final: 0.7644 (mt0) REVERT: E 373 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7406 (p0) REVERT: E 416 ASP cc_start: 0.7750 (t70) cc_final: 0.7465 (t0) REVERT: E 428 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8374 (mmtt) outliers start: 77 outliers final: 41 residues processed: 229 average time/residue: 0.7216 time to fit residues: 190.1939 Evaluate side-chains 213 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 373 ASP Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 147 optimal weight: 0.7980 chunk 225 optimal weight: 0.2980 chunk 284 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 228 optimal weight: 0.1980 chunk 296 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.161495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112190 restraints weight = 30781.866| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.89 r_work: 0.3222 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25890 Z= 0.100 Angle : 0.527 10.840 35118 Z= 0.273 Chirality : 0.044 0.153 3978 Planarity : 0.003 0.032 4476 Dihedral : 4.886 31.148 3426 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.03 % Favored : 93.78 % Rotamer: Outliers : 2.21 % Allowed : 17.50 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.24 (0.15), residues: 3168 helix: 1.30 (0.17), residues: 1080 sheet: -0.52 (0.20), residues: 648 loop : -1.09 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 130 TYR 0.012 0.001 TYR E 318 PHE 0.008 0.001 PHE C 225 TRP 0.010 0.001 TRP E 290 HIS 0.006 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00223 (25890) covalent geometry : angle 0.52715 (35118) hydrogen bonds : bond 0.03404 ( 876) hydrogen bonds : angle 4.39263 ( 2502) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: F 145 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8004 (mm-30) REVERT: F 150 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.6992 (mpt-90) REVERT: F 154 GLN cc_start: 0.7875 (mm110) cc_final: 0.7534 (mt0) REVERT: F 163 ASP cc_start: 0.8406 (t70) cc_final: 0.8137 (t70) REVERT: F 281 LYS cc_start: 0.7370 (tttm) cc_final: 0.6962 (ptmt) REVERT: F 416 ASP cc_start: 0.7613 (t70) cc_final: 0.7350 (t70) REVERT: A 154 GLN cc_start: 0.7693 (mm110) cc_final: 0.7396 (mt0) REVERT: A 260 GLN cc_start: 0.8094 (tt0) cc_final: 0.7840 (tt0) REVERT: A 337 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8229 (mm) REVERT: B 154 GLN cc_start: 0.7795 (mm110) cc_final: 0.7524 (mt0) REVERT: B 260 GLN cc_start: 0.8007 (tt0) cc_final: 0.7763 (tt0) REVERT: B 337 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8309 (mm) REVERT: B 425 ASP cc_start: 0.8034 (t0) cc_final: 0.7811 (t0) REVERT: C 154 GLN cc_start: 0.7827 (mm110) cc_final: 0.7519 (mt0) REVERT: C 281 LYS cc_start: 0.7331 (tttm) cc_final: 0.6902 (ptmt) REVERT: D 150 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7822 (mpt-90) REVERT: D 154 GLN cc_start: 0.7850 (mm110) cc_final: 0.7649 (mt0) REVERT: D 373 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7262 (p0) REVERT: E 150 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7418 (mpt-90) REVERT: E 154 GLN cc_start: 0.7876 (mm110) cc_final: 0.7587 (mt0) REVERT: E 373 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7390 (p0) REVERT: E 416 ASP cc_start: 0.7663 (t70) cc_final: 0.7390 (t0) REVERT: E 428 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8331 (mmtt) outliers start: 61 outliers final: 35 residues processed: 219 average time/residue: 0.7254 time to fit residues: 182.8017 Evaluate side-chains 207 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 282 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 252 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.155613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102894 restraints weight = 30066.143| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.93 r_work: 0.3102 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25890 Z= 0.160 Angle : 0.580 9.145 35118 Z= 0.305 Chirality : 0.047 0.185 3978 Planarity : 0.004 0.031 4476 Dihedral : 5.089 30.306 3426 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.66 % Favored : 93.15 % Rotamer: Outliers : 2.28 % Allowed : 17.64 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.36 (0.15), residues: 3168 helix: 1.18 (0.16), residues: 1080 sheet: -0.49 (0.19), residues: 666 loop : -1.20 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 211 TYR 0.013 0.001 TYR E 318 PHE 0.012 0.001 PHE D 225 TRP 0.011 0.002 TRP F 230 HIS 0.007 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00387 (25890) covalent geometry : angle 0.58003 (35118) hydrogen bonds : bond 0.04235 ( 876) hydrogen bonds : angle 4.59438 ( 2502) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7929 (mm110) cc_final: 0.7608 (mt0) REVERT: F 163 ASP cc_start: 0.8393 (t70) cc_final: 0.8152 (t70) REVERT: F 281 LYS cc_start: 0.7400 (tttm) cc_final: 0.6926 (ptmt) REVERT: F 416 ASP cc_start: 0.7618 (t70) cc_final: 0.7361 (t70) REVERT: A 154 GLN cc_start: 0.7752 (mm110) cc_final: 0.7447 (mt0) REVERT: A 322 GLU cc_start: 0.8388 (mp0) cc_final: 0.8060 (mp0) REVERT: A 337 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8239 (mm) REVERT: B 154 GLN cc_start: 0.7847 (mm110) cc_final: 0.7561 (mt0) REVERT: B 337 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 425 ASP cc_start: 0.8032 (t0) cc_final: 0.7794 (t0) REVERT: B 428 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7996 (mttm) REVERT: C 154 GLN cc_start: 0.7884 (mm110) cc_final: 0.7564 (mt0) REVERT: C 347 TYR cc_start: 0.8585 (m-80) cc_final: 0.8307 (m-80) REVERT: D 150 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7543 (mpt-90) REVERT: D 154 GLN cc_start: 0.7884 (mm110) cc_final: 0.7610 (mt0) REVERT: D 373 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7354 (p0) REVERT: E 150 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7358 (mpt-90) REVERT: E 154 GLN cc_start: 0.7923 (mm110) cc_final: 0.7607 (mt0) REVERT: E 373 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7405 (p0) REVERT: E 416 ASP cc_start: 0.7713 (t70) cc_final: 0.7427 (t0) REVERT: E 428 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8287 (mmtt) outliers start: 63 outliers final: 41 residues processed: 219 average time/residue: 0.6826 time to fit residues: 172.6577 Evaluate side-chains 211 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 439 SER Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 242 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 158 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 312 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.157689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106959 restraints weight = 30364.600| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.89 r_work: 0.3150 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25890 Z= 0.108 Angle : 0.537 10.273 35118 Z= 0.279 Chirality : 0.045 0.160 3978 Planarity : 0.003 0.032 4476 Dihedral : 4.922 31.248 3426 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.16 % Favored : 93.66 % Rotamer: Outliers : 1.95 % Allowed : 18.00 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.20 (0.15), residues: 3168 helix: 1.37 (0.17), residues: 1080 sheet: -0.50 (0.20), residues: 648 loop : -1.11 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 150 TYR 0.013 0.001 TYR E 318 PHE 0.008 0.001 PHE D 225 TRP 0.008 0.001 TRP F 230 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00248 (25890) covalent geometry : angle 0.53722 (35118) hydrogen bonds : bond 0.03537 ( 876) hydrogen bonds : angle 4.41142 ( 2502) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: F 150 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.6832 (mpt-90) REVERT: F 154 GLN cc_start: 0.7885 (mm110) cc_final: 0.7580 (mt0) REVERT: F 163 ASP cc_start: 0.8428 (t70) cc_final: 0.8168 (t70) REVERT: F 281 LYS cc_start: 0.7420 (tttm) cc_final: 0.6977 (ptmt) REVERT: F 416 ASP cc_start: 0.7611 (t70) cc_final: 0.7361 (t70) REVERT: A 154 GLN cc_start: 0.7698 (mm110) cc_final: 0.7410 (mt0) REVERT: A 260 GLN cc_start: 0.8101 (tt0) cc_final: 0.7844 (tt0) REVERT: A 337 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 154 GLN cc_start: 0.7796 (mm110) cc_final: 0.7532 (mt0) REVERT: B 260 GLN cc_start: 0.8005 (tt0) cc_final: 0.7758 (tt0) REVERT: B 337 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8268 (mm) REVERT: B 425 ASP cc_start: 0.7995 (t0) cc_final: 0.7740 (t70) REVERT: B 428 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7985 (mttm) REVERT: C 154 GLN cc_start: 0.7816 (mm110) cc_final: 0.7533 (mt0) REVERT: C 281 LYS cc_start: 0.7358 (tttm) cc_final: 0.6978 (ptmt) REVERT: C 347 TYR cc_start: 0.8619 (m-80) cc_final: 0.8314 (m-80) REVERT: D 150 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7791 (mpt-90) REVERT: D 373 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7259 (p0) REVERT: E 150 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7398 (mpt-90) REVERT: E 154 GLN cc_start: 0.7874 (mm110) cc_final: 0.7608 (mt0) REVERT: E 373 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7378 (p0) REVERT: E 416 ASP cc_start: 0.7639 (t70) cc_final: 0.7363 (t0) REVERT: E 428 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8292 (mmtt) outliers start: 54 outliers final: 40 residues processed: 210 average time/residue: 0.7155 time to fit residues: 173.0946 Evaluate side-chains 210 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 175 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 171 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 256 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 278 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.156177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103582 restraints weight = 30139.234| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.93 r_work: 0.3102 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25890 Z= 0.142 Angle : 0.569 9.526 35118 Z= 0.297 Chirality : 0.046 0.177 3978 Planarity : 0.004 0.031 4476 Dihedral : 5.018 30.933 3426 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.63 % Favored : 93.18 % Rotamer: Outliers : 1.99 % Allowed : 17.86 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.26 (0.15), residues: 3168 helix: 1.30 (0.16), residues: 1080 sheet: -0.44 (0.19), residues: 666 loop : -1.17 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 130 TYR 0.015 0.001 TYR E 318 PHE 0.011 0.001 PHE D 225 TRP 0.012 0.002 TRP F 230 HIS 0.007 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00341 (25890) covalent geometry : angle 0.56874 (35118) hydrogen bonds : bond 0.03999 ( 876) hydrogen bonds : angle 4.52602 ( 2502) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7913 (mm110) cc_final: 0.7603 (mt0) REVERT: F 163 ASP cc_start: 0.8404 (t70) cc_final: 0.8143 (t70) REVERT: F 281 LYS cc_start: 0.7435 (tttm) cc_final: 0.6957 (ptmt) REVERT: F 416 ASP cc_start: 0.7601 (t70) cc_final: 0.7339 (t70) REVERT: A 154 GLN cc_start: 0.7731 (mm110) cc_final: 0.7438 (mt0) REVERT: A 322 GLU cc_start: 0.8321 (mp0) cc_final: 0.8013 (mp0) REVERT: A 337 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 154 GLN cc_start: 0.7819 (mm110) cc_final: 0.7545 (mt0) REVERT: B 337 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8296 (mm) REVERT: B 425 ASP cc_start: 0.7993 (t0) cc_final: 0.7722 (t70) REVERT: B 428 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7926 (mttm) REVERT: C 154 GLN cc_start: 0.7840 (mm110) cc_final: 0.7546 (mt0) REVERT: C 281 LYS cc_start: 0.7323 (tttm) cc_final: 0.6933 (ptmt) REVERT: C 347 TYR cc_start: 0.8581 (m-80) cc_final: 0.8272 (m-80) REVERT: D 373 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7346 (p0) REVERT: E 150 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7368 (mpt-90) REVERT: E 154 GLN cc_start: 0.7912 (mm110) cc_final: 0.7616 (mt0) REVERT: E 373 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7404 (p0) REVERT: E 416 ASP cc_start: 0.7698 (t70) cc_final: 0.7438 (t0) REVERT: E 428 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8248 (mmtt) outliers start: 55 outliers final: 39 residues processed: 214 average time/residue: 0.7111 time to fit residues: 176.1498 Evaluate side-chains 209 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 428 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 90 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.155842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103388 restraints weight = 30013.961| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.92 r_work: 0.3110 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25890 Z= 0.149 Angle : 0.574 9.106 35118 Z= 0.301 Chirality : 0.046 0.185 3978 Planarity : 0.004 0.032 4476 Dihedral : 5.090 31.078 3426 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.98 % Favored : 92.83 % Rotamer: Outliers : 1.92 % Allowed : 18.04 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.26 (0.15), residues: 3168 helix: 1.28 (0.16), residues: 1080 sheet: -0.35 (0.19), residues: 654 loop : -1.20 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 211 TYR 0.017 0.001 TYR E 318 PHE 0.011 0.001 PHE D 225 TRP 0.011 0.002 TRP F 230 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00358 (25890) covalent geometry : angle 0.57442 (35118) hydrogen bonds : bond 0.04086 ( 876) hydrogen bonds : angle 4.56254 ( 2502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9432.49 seconds wall clock time: 161 minutes 53.32 seconds (9713.32 seconds total)