Starting phenix.real_space_refine on Sat May 24 07:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hzx_35091/05_2025/8hzx_35091.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hzx_35091/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hzx_35091/05_2025/8hzx_35091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hzx_35091/05_2025/8hzx_35091.map" model { file = "/net/cci-nas-00/data/ceres_data/8hzx_35091/05_2025/8hzx_35091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hzx_35091/05_2025/8hzx_35091.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25320 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, F Time building chain proxies: 10.14, per 1000 atoms: 0.40 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: 5.99 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 3.47 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: 8.81 Time building geometry restraints manager: 6.97 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 2.010 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: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 50.320 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (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 TRP 0.009 0.002 TRP E 230 HIS 0.007 0.001 HIS D 228 PHE 0.010 0.002 PHE E 315 TYR 0.016 0.002 TYR D 174 ARG 0.006 0.001 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.18709 ( 876) hydrogen bonds : angle 7.16466 ( 2502) covalent geometry : bond 0.00644 (25890) covalent geometry : angle 0.76841 (35118) *********************** 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 : 3.004 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: 1.6588 time to fit residues: 394.5994 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 : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 HIS F 160 ASN F 243 GLN A 160 ASN A 243 GLN B 39 HIS B 160 ASN B 243 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109926 restraints weight = 30618.408| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.91 r_work: 0.3190 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1006 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= 0.169 Angle : 0.592 6.396 35118 Z= 0.318 Chirality : 0.047 0.180 3978 Planarity : 0.004 0.031 4476 Dihedral : 5.261 27.305 3426 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.00 % Favored : 93.81 % Rotamer: Outliers : 3.43 % Allowed : 12.73 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3168 helix: 0.45 (0.16), residues: 1086 sheet: -0.70 (0.20), residues: 600 loop : -1.19 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 230 HIS 0.007 0.001 HIS B 228 PHE 0.012 0.001 PHE E 225 TYR 0.010 0.002 TYR A 174 ARG 0.004 0.001 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04861 ( 876) hydrogen bonds : angle 5.10432 ( 2502) covalent geometry : bond 0.00401 (25890) covalent geometry : angle 0.59239 (35118) *********************** 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 269 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 174 time to evaluate : 3.033 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8484 (mtm) cc_final: 0.8264 (mtm) REVERT: F 150 ARG cc_start: 0.8327 (mmt90) cc_final: 0.7904 (mtm-85) REVERT: F 154 GLN cc_start: 0.7971 (mm110) cc_final: 0.7585 (mt0) REVERT: F 163 ASP cc_start: 0.8316 (t70) cc_final: 0.8022 (t70) REVERT: F 281 LYS cc_start: 0.7291 (tttm) cc_final: 0.6953 (ptmt) REVERT: F 320 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6839 (ppp) REVERT: A 154 GLN cc_start: 0.7882 (mm110) cc_final: 0.7461 (mt0) REVERT: B 154 GLN cc_start: 0.7994 (mm110) cc_final: 0.7560 (mt0) REVERT: B 373 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7573 (p0) REVERT: C 58 MET cc_start: 0.8282 (mtm) cc_final: 0.7991 (mtt) REVERT: C 154 GLN cc_start: 0.7929 (mm110) cc_final: 0.7566 (mt0) REVERT: C 163 ASP cc_start: 0.8244 (t70) cc_final: 0.7952 (t70) REVERT: C 281 LYS cc_start: 0.7497 (tttm) cc_final: 0.7062 (ptmt) REVERT: C 347 TYR cc_start: 0.8628 (m-80) cc_final: 0.8404 (m-80) REVERT: C 428 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8454 (mptt) REVERT: D 85 MET cc_start: 0.8976 (mtt) cc_final: 0.8560 (mtt) REVERT: D 154 GLN cc_start: 0.8094 (mm110) cc_final: 0.7711 (mt0) REVERT: D 373 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7348 (p0) REVERT: E 85 MET cc_start: 0.8945 (mtt) cc_final: 0.8552 (mtt) REVERT: E 154 GLN cc_start: 0.8107 (mm110) cc_final: 0.7750 (mt0) REVERT: E 320 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6715 (ppp) REVERT: E 373 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7509 (p0) REVERT: E 416 ASP cc_start: 0.7863 (t0) cc_final: 0.7605 (t0) REVERT: E 428 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8380 (mmtt) outliers start: 95 outliers final: 31 residues processed: 253 average time/residue: 1.3462 time to fit residues: 394.4455 Evaluate side-chains 197 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 2.692 ------------------------------------------------------------------------------- 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 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 314 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 314 VAL 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 C residue 175 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 285 MET 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 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 320 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 440 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 204 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 295 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.161582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111422 restraints weight = 30547.571| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.90 r_work: 0.3218 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25890 Z= 0.116 Angle : 0.537 8.909 35118 Z= 0.284 Chirality : 0.045 0.160 3978 Planarity : 0.004 0.030 4476 Dihedral : 5.004 27.286 3426 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.91 % Rotamer: Outliers : 2.60 % Allowed : 14.57 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3168 helix: 0.78 (0.16), residues: 1086 sheet: -0.62 (0.19), residues: 666 loop : -1.01 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 290 HIS 0.006 0.001 HIS B 228 PHE 0.010 0.001 PHE E 225 TYR 0.008 0.001 TYR C 318 ARG 0.003 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 876) hydrogen bonds : angle 4.72041 ( 2502) covalent geometry : bond 0.00265 (25890) covalent geometry : angle 0.53713 (35118) *********************** 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 244 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 2.781 Fit side-chains REVERT: F 58 MET cc_start: 0.8435 (mtm) cc_final: 0.8208 (mtm) REVERT: F 150 ARG cc_start: 0.8281 (mmt90) cc_final: 0.7900 (mtm-85) REVERT: F 154 GLN cc_start: 0.7904 (mm110) cc_final: 0.7543 (mt0) REVERT: F 163 ASP cc_start: 0.8346 (t70) cc_final: 0.8062 (t70) REVERT: F 281 LYS cc_start: 0.7351 (tttm) cc_final: 0.6909 (ptmt) REVERT: F 320 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6837 (ppp) REVERT: F 416 ASP cc_start: 0.7635 (t0) cc_final: 0.7400 (t70) REVERT: A 154 GLN cc_start: 0.7775 (mm110) cc_final: 0.7382 (mt0) REVERT: A 197 MET cc_start: 0.8497 (mmp) cc_final: 0.8154 (mmp) REVERT: B 154 GLN cc_start: 0.7886 (mm110) cc_final: 0.7505 (mt0) REVERT: B 197 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8137 (mmp) REVERT: B 373 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7534 (p0) REVERT: B 425 ASP cc_start: 0.8190 (t0) cc_final: 0.7885 (t70) REVERT: C 58 MET cc_start: 0.8233 (mtm) cc_final: 0.7978 (mtt) REVERT: C 154 GLN cc_start: 0.7909 (mm110) cc_final: 0.7510 (mt0) REVERT: C 163 ASP cc_start: 0.8266 (t70) cc_final: 0.7974 (t70) REVERT: C 281 LYS cc_start: 0.7484 (tttm) cc_final: 0.6869 (ptmt) REVERT: C 320 MET cc_start: 0.7069 (ppp) cc_final: 0.6702 (pmm) REVERT: C 347 TYR cc_start: 0.8646 (m-80) cc_final: 0.8384 (m-80) REVERT: C 362 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8103 (pt) REVERT: D 85 MET cc_start: 0.8973 (mtt) cc_final: 0.8528 (mtt) REVERT: D 154 GLN cc_start: 0.7987 (mm110) cc_final: 0.7679 (mt0) REVERT: D 373 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7331 (p0) REVERT: E 85 MET cc_start: 0.8953 (mtt) cc_final: 0.8511 (mtt) REVERT: E 154 GLN cc_start: 0.7993 (mm110) cc_final: 0.7666 (mt0) REVERT: E 373 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7432 (p0) REVERT: E 416 ASP cc_start: 0.7721 (t0) cc_final: 0.7286 (t0) outliers start: 72 outliers final: 37 residues processed: 231 average time/residue: 1.3099 time to fit residues: 353.1767 Evaluate side-chains 205 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 3.111 ------------------------------------------------------------------------------- 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 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 439 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 ILE 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 197 MET Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 373 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 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 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 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 373 ASP Chi-restraints excluded: chain E residue 424 THR 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 269 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 189 HIS A 39 HIS A 108 HIS B 108 HIS C 189 HIS D 189 HIS E 189 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107383 restraints weight = 30970.471| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.89 r_work: 0.3161 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25890 Z= 0.201 Angle : 0.623 7.856 35118 Z= 0.332 Chirality : 0.049 0.198 3978 Planarity : 0.004 0.032 4476 Dihedral : 5.293 26.481 3426 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.28 % Rotamer: Outliers : 2.71 % Allowed : 14.79 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3168 helix: 0.77 (0.16), residues: 1086 sheet: -0.63 (0.19), residues: 666 loop : -1.18 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 437 HIS 0.007 0.001 HIS A 228 PHE 0.013 0.002 PHE D 225 TYR 0.010 0.002 TYR C 104 ARG 0.003 0.001 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 876) hydrogen bonds : angle 4.87797 ( 2502) covalent geometry : bond 0.00491 (25890) covalent geometry : angle 0.62268 (35118) *********************** 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 240 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 165 time to evaluate : 2.898 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8527 (mtm) cc_final: 0.8300 (mtm) REVERT: F 154 GLN cc_start: 0.7981 (mm110) cc_final: 0.7610 (mt0) REVERT: F 163 ASP cc_start: 0.8384 (t70) cc_final: 0.8142 (t70) REVERT: F 281 LYS cc_start: 0.7406 (tttm) cc_final: 0.7009 (ptmt) REVERT: F 320 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6965 (ppp) REVERT: F 428 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8152 (mttm) REVERT: A 154 GLN cc_start: 0.7890 (mm110) cc_final: 0.7550 (mt0) REVERT: A 337 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 154 GLN cc_start: 0.7970 (mm110) cc_final: 0.7576 (mt0) REVERT: B 260 GLN cc_start: 0.8129 (tt0) cc_final: 0.7860 (tt0) REVERT: B 322 GLU cc_start: 0.8627 (mp0) cc_final: 0.8360 (mp0) REVERT: B 337 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8379 (mm) REVERT: B 425 ASP cc_start: 0.8121 (t0) cc_final: 0.7920 (t70) REVERT: C 154 GLN cc_start: 0.7986 (mm110) cc_final: 0.7632 (mt0) REVERT: C 163 ASP cc_start: 0.8309 (t70) cc_final: 0.8055 (t70) REVERT: D 85 MET cc_start: 0.8968 (mtt) cc_final: 0.8590 (mtt) REVERT: D 154 GLN cc_start: 0.8026 (mm110) cc_final: 0.7728 (mt0) REVERT: D 322 GLU cc_start: 0.8687 (mp0) cc_final: 0.8318 (mp0) REVERT: D 373 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7372 (p0) REVERT: E 85 MET cc_start: 0.8939 (mtt) cc_final: 0.8564 (mtt) REVERT: E 154 GLN cc_start: 0.8011 (mm110) cc_final: 0.7688 (mt0) REVERT: E 373 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7457 (p0) REVERT: E 416 ASP cc_start: 0.7854 (t0) cc_final: 0.7581 (t0) REVERT: E 428 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8459 (mmtm) outliers start: 75 outliers final: 45 residues processed: 227 average time/residue: 1.2851 time to fit residues: 340.9339 Evaluate side-chains 214 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 2.793 ------------------------------------------------------------------------------- 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 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 A residue 227 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 362 ILE 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 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 B residue 440 SER 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 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 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 285 MET 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 D residue 440 SER Chi-restraints excluded: chain D residue 461 MET 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 428 LYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 67 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 0.0870 chunk 234 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 258 optimal weight: 9.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.161211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111395 restraints weight = 30936.115| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.90 r_work: 0.3217 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25890 Z= 0.110 Angle : 0.534 9.533 35118 Z= 0.279 Chirality : 0.045 0.163 3978 Planarity : 0.004 0.030 4476 Dihedral : 4.982 28.439 3426 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.12 % Favored : 93.69 % Rotamer: Outliers : 2.31 % Allowed : 16.70 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3168 helix: 1.10 (0.17), residues: 1086 sheet: -0.57 (0.19), residues: 660 loop : -1.08 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 290 HIS 0.006 0.001 HIS B 228 PHE 0.008 0.001 PHE D 225 TYR 0.009 0.001 TYR E 318 ARG 0.003 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 876) hydrogen bonds : angle 4.54269 ( 2502) covalent geometry : bond 0.00251 (25890) covalent geometry : angle 0.53382 (35118) *********************** 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 230 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 3.060 Fit side-chains revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7908 (mm110) cc_final: 0.7544 (mt0) REVERT: F 163 ASP cc_start: 0.8396 (t70) cc_final: 0.8131 (t70) REVERT: F 281 LYS cc_start: 0.7443 (tttm) cc_final: 0.7032 (ptmt) REVERT: F 416 ASP cc_start: 0.7612 (t0) cc_final: 0.7361 (t70) REVERT: A 154 GLN cc_start: 0.7682 (mm110) cc_final: 0.7359 (mt0) REVERT: A 260 GLN cc_start: 0.8117 (tt0) cc_final: 0.7853 (tt0) REVERT: A 337 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 154 GLN cc_start: 0.7795 (mm110) cc_final: 0.7509 (mt0) REVERT: B 260 GLN cc_start: 0.8042 (tt0) cc_final: 0.7793 (tt0) REVERT: B 337 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8266 (mm) REVERT: B 425 ASP cc_start: 0.8063 (t0) cc_final: 0.7855 (t0) REVERT: C 154 GLN cc_start: 0.7849 (mm110) cc_final: 0.7470 (mt0) REVERT: C 163 ASP cc_start: 0.8350 (t70) cc_final: 0.8070 (t70) REVERT: C 281 LYS cc_start: 0.7253 (tttm) cc_final: 0.6897 (ptmt) REVERT: C 320 MET cc_start: 0.7039 (ppp) cc_final: 0.6722 (pmm) REVERT: D 85 MET cc_start: 0.8947 (mtt) cc_final: 0.8499 (mtt) REVERT: D 154 GLN cc_start: 0.7928 (mm110) cc_final: 0.7676 (mt0) REVERT: D 373 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7328 (p0) REVERT: E 85 MET cc_start: 0.8908 (mtt) cc_final: 0.8458 (mtt) REVERT: E 150 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7398 (mpt-90) REVERT: E 154 GLN cc_start: 0.7940 (mm110) cc_final: 0.7649 (mt0) REVERT: E 373 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7350 (p0) REVERT: E 416 ASP cc_start: 0.7706 (t0) cc_final: 0.7449 (t0) REVERT: E 428 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8352 (mmtt) outliers start: 64 outliers final: 43 residues processed: 221 average time/residue: 1.2850 time to fit residues: 332.7254 Evaluate side-chains 209 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 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 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 A residue 438 VAL 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 337 LEU Chi-restraints excluded: chain B residue 362 ILE 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 373 ASP Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 438 VAL 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 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 Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 186 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 246 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109677 restraints weight = 30691.969| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.90 r_work: 0.3189 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25890 Z= 0.141 Angle : 0.562 9.319 35118 Z= 0.295 Chirality : 0.046 0.175 3978 Planarity : 0.004 0.031 4476 Dihedral : 5.029 27.957 3426 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.60 % Favored : 93.21 % Rotamer: Outliers : 2.39 % Allowed : 16.56 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3168 helix: 1.10 (0.16), residues: 1080 sheet: -0.49 (0.19), residues: 666 loop : -1.12 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 230 HIS 0.006 0.001 HIS B 228 PHE 0.011 0.001 PHE D 225 TYR 0.013 0.001 TYR E 318 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 876) hydrogen bonds : angle 4.60581 ( 2502) covalent geometry : bond 0.00334 (25890) covalent geometry : angle 0.56210 (35118) *********************** 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 232 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 3.082 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8360 (mtm) cc_final: 0.8115 (ttm) REVERT: F 154 GLN cc_start: 0.7940 (mm110) cc_final: 0.7611 (mt0) REVERT: F 163 ASP cc_start: 0.8401 (t70) cc_final: 0.8141 (t70) REVERT: F 281 LYS cc_start: 0.7366 (tttm) cc_final: 0.6948 (ptmt) REVERT: F 416 ASP cc_start: 0.7630 (t70) cc_final: 0.7377 (t70) REVERT: A 154 GLN cc_start: 0.7733 (mm110) cc_final: 0.7439 (mt0) REVERT: B 154 GLN cc_start: 0.7818 (mm110) cc_final: 0.7544 (mt0) REVERT: B 260 GLN cc_start: 0.8044 (tt0) cc_final: 0.7799 (tt0) REVERT: B 373 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7494 (p0) REVERT: B 425 ASP cc_start: 0.8070 (t0) cc_final: 0.7828 (t0) REVERT: C 154 GLN cc_start: 0.7883 (mm110) cc_final: 0.7522 (mt0) REVERT: C 163 ASP cc_start: 0.8345 (t70) cc_final: 0.8081 (t70) REVERT: C 281 LYS cc_start: 0.7313 (tttm) cc_final: 0.6943 (ptmt) REVERT: D 85 MET cc_start: 0.8947 (mtt) cc_final: 0.8544 (mtt) REVERT: D 150 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7604 (mpt-90) REVERT: D 154 GLN cc_start: 0.7940 (mm110) cc_final: 0.7697 (mt0) REVERT: D 373 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7327 (p0) REVERT: E 85 MET cc_start: 0.8914 (mtt) cc_final: 0.8575 (mtt) REVERT: E 150 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7359 (mpt-90) REVERT: E 154 GLN cc_start: 0.7945 (mm110) cc_final: 0.7634 (mt0) REVERT: E 373 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7394 (p0) REVERT: E 416 ASP cc_start: 0.7729 (t0) cc_final: 0.7476 (t0) REVERT: E 428 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8422 (mmtm) outliers start: 66 outliers final: 46 residues processed: 222 average time/residue: 1.2868 time to fit residues: 334.6851 Evaluate side-chains 214 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 2.896 ------------------------------------------------------------------------------- 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 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 362 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 438 VAL 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 373 ASP Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 440 SER 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 C residue 440 SER 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 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 D residue 440 SER 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 Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 238 optimal weight: 3.9990 chunk 182 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 186 optimal weight: 0.1980 chunk 312 optimal weight: 30.0000 chunk 163 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 0.2980 chunk 313 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 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 = 0.3976 r_free = 0.3976 target = 0.162471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112938 restraints weight = 30931.926| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.91 r_work: 0.3243 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25890 Z= 0.098 Angle : 0.520 11.111 35118 Z= 0.268 Chirality : 0.044 0.148 3978 Planarity : 0.003 0.030 4476 Dihedral : 4.795 29.473 3426 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.68 % Favored : 94.13 % Rotamer: Outliers : 2.31 % Allowed : 17.06 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3168 helix: 1.30 (0.17), residues: 1080 sheet: -0.43 (0.20), residues: 642 loop : -1.00 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 290 HIS 0.006 0.001 HIS B 228 PHE 0.008 0.001 PHE F 315 TYR 0.013 0.001 TYR C 318 ARG 0.003 0.000 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 876) hydrogen bonds : angle 4.37974 ( 2502) covalent geometry : bond 0.00220 (25890) covalent geometry : angle 0.51950 (35118) *********************** 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 235 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 2.987 Fit side-chains revert: symmetry clash REVERT: F 150 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.6885 (mpt-90) REVERT: F 154 GLN cc_start: 0.7859 (mm110) cc_final: 0.7533 (mt0) REVERT: F 163 ASP cc_start: 0.8408 (t70) cc_final: 0.8144 (t70) REVERT: F 281 LYS cc_start: 0.7434 (tttm) cc_final: 0.7023 (ptmt) REVERT: F 322 GLU cc_start: 0.8269 (mp0) cc_final: 0.8066 (mp0) REVERT: F 416 ASP cc_start: 0.7626 (t70) cc_final: 0.7373 (t70) REVERT: A 154 GLN cc_start: 0.7680 (mm110) cc_final: 0.7402 (mt0) REVERT: A 260 GLN cc_start: 0.8096 (tt0) cc_final: 0.7836 (tt0) REVERT: A 337 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8204 (mm) REVERT: B 154 GLN cc_start: 0.7764 (mm110) cc_final: 0.7496 (mt0) REVERT: B 260 GLN cc_start: 0.8015 (tt0) cc_final: 0.7762 (tt0) REVERT: B 425 ASP cc_start: 0.8006 (t0) cc_final: 0.7779 (t0) REVERT: C 154 GLN cc_start: 0.7863 (mm110) cc_final: 0.7577 (mt0) REVERT: C 281 LYS cc_start: 0.7303 (tttm) cc_final: 0.7024 (ptmt) REVERT: C 335 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: D 85 MET cc_start: 0.8923 (mtt) cc_final: 0.8503 (mtt) REVERT: D 154 GLN cc_start: 0.7858 (mm110) cc_final: 0.7644 (mt0) REVERT: D 373 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7326 (p0) REVERT: E 85 MET cc_start: 0.8912 (mtt) cc_final: 0.8491 (mtt) REVERT: E 150 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7429 (mpt-90) REVERT: E 154 GLN cc_start: 0.7899 (mm110) cc_final: 0.7618 (mt0) REVERT: E 373 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7350 (p0) REVERT: E 416 ASP cc_start: 0.7693 (t0) cc_final: 0.7198 (t0) REVERT: E 428 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8296 (mmtt) outliers start: 64 outliers final: 35 residues processed: 229 average time/residue: 1.3537 time to fit residues: 359.3234 Evaluate side-chains 208 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 2.698 ------------------------------------------------------------------------------- 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 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 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 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 440 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 227 VAL 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 440 SER 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 D residue 440 SER Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 175 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 Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 147 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 307 optimal weight: 0.0170 chunk 47 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 277 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 overall best weight: 1.3022 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.160003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109999 restraints weight = 30683.382| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.89 r_work: 0.3198 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25890 Z= 0.141 Angle : 0.560 9.717 35118 Z= 0.292 Chirality : 0.046 0.173 3978 Planarity : 0.004 0.030 4476 Dihedral : 4.935 28.763 3426 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.28 % Rotamer: Outliers : 2.68 % Allowed : 16.85 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3168 helix: 1.47 (0.16), residues: 1044 sheet: -0.43 (0.19), residues: 666 loop : -1.21 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 230 HIS 0.007 0.001 HIS A 228 PHE 0.011 0.001 PHE D 225 TYR 0.013 0.001 TYR E 318 ARG 0.002 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 876) hydrogen bonds : angle 4.53374 ( 2502) covalent geometry : bond 0.00338 (25890) covalent geometry : angle 0.56047 (35118) *********************** 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 242 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 168 time to evaluate : 2.924 Fit side-chains revert: symmetry clash REVERT: F 145 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8018 (mm-30) REVERT: F 150 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.6829 (mpt-90) REVERT: F 154 GLN cc_start: 0.7963 (mm110) cc_final: 0.7661 (mt0) REVERT: F 163 ASP cc_start: 0.8410 (t70) cc_final: 0.8150 (t70) REVERT: F 281 LYS cc_start: 0.7485 (tttm) cc_final: 0.7034 (ptmt) REVERT: F 320 MET cc_start: 0.6835 (ppp) cc_final: 0.6488 (ppp) REVERT: F 416 ASP cc_start: 0.7633 (t70) cc_final: 0.7380 (t70) REVERT: A 154 GLN cc_start: 0.7704 (mm110) cc_final: 0.7433 (mt0) REVERT: A 337 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8267 (mm) REVERT: B 154 GLN cc_start: 0.7791 (mm110) cc_final: 0.7534 (mt0) REVERT: B 260 GLN cc_start: 0.8043 (tt0) cc_final: 0.7801 (tt0) REVERT: B 322 GLU cc_start: 0.8391 (mp0) cc_final: 0.8166 (mp0) REVERT: B 425 ASP cc_start: 0.8049 (t0) cc_final: 0.7817 (t0) REVERT: C 154 GLN cc_start: 0.7927 (mm110) cc_final: 0.7650 (mt0) REVERT: C 281 LYS cc_start: 0.7361 (tttm) cc_final: 0.6999 (ptmt) REVERT: C 335 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: C 347 TYR cc_start: 0.8647 (m-80) cc_final: 0.8367 (m-80) REVERT: D 85 MET cc_start: 0.8958 (mtt) cc_final: 0.8487 (mtt) REVERT: D 154 GLN cc_start: 0.7872 (mm110) cc_final: 0.7639 (mt0) REVERT: D 373 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7290 (p0) REVERT: E 150 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7379 (mpt-90) REVERT: E 154 GLN cc_start: 0.7924 (mm110) cc_final: 0.7618 (mt0) REVERT: E 373 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7366 (p0) REVERT: E 416 ASP cc_start: 0.7697 (t0) cc_final: 0.7209 (t0) REVERT: E 428 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8385 (mmtm) outliers start: 74 outliers final: 43 residues processed: 231 average time/residue: 1.3486 time to fit residues: 361.6675 Evaluate side-chains 208 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 2.818 ------------------------------------------------------------------------------- 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 438 VAL 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 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 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 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 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 D residue 440 SER 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 Chi-restraints excluded: chain E residue 440 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 290 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.154168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102437 restraints weight = 30366.788| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.89 r_work: 0.3072 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25890 Z= 0.233 Angle : 0.653 8.111 35118 Z= 0.346 Chirality : 0.050 0.212 3978 Planarity : 0.004 0.036 4476 Dihedral : 5.384 28.657 3426 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.61 % Favored : 92.20 % Rotamer: Outliers : 2.53 % Allowed : 17.21 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3168 helix: 1.20 (0.16), residues: 1044 sheet: -0.53 (0.19), residues: 654 loop : -1.41 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 230 HIS 0.008 0.001 HIS A 228 PHE 0.014 0.002 PHE D 225 TYR 0.015 0.002 TYR E 318 ARG 0.003 0.001 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.05006 ( 876) hydrogen bonds : angle 4.87179 ( 2502) covalent geometry : bond 0.00572 (25890) covalent geometry : angle 0.65343 (35118) *********************** 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 239 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 169 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 31 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8161 (mm) REVERT: F 154 GLN cc_start: 0.7998 (mm110) cc_final: 0.7709 (mt0) REVERT: F 163 ASP cc_start: 0.8462 (t70) cc_final: 0.8239 (t70) REVERT: F 235 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8649 (mtm) REVERT: A 154 GLN cc_start: 0.7925 (mm110) cc_final: 0.7623 (mt0) REVERT: A 322 GLU cc_start: 0.8624 (mp0) cc_final: 0.8281 (mp0) REVERT: A 337 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8302 (mm) REVERT: A 365 GLU cc_start: 0.7951 (mp0) cc_final: 0.7585 (mp0) REVERT: B 154 GLN cc_start: 0.7896 (mm110) cc_final: 0.7645 (mt0) REVERT: B 322 GLU cc_start: 0.8597 (mp0) cc_final: 0.8320 (mp0) REVERT: B 337 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8366 (mm) REVERT: B 425 ASP cc_start: 0.8080 (t0) cc_final: 0.7838 (t0) REVERT: C 31 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8276 (mm) REVERT: C 154 GLN cc_start: 0.7931 (mm110) cc_final: 0.7597 (mt0) REVERT: C 163 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8127 (t70) REVERT: C 235 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8625 (mtm) REVERT: C 347 TYR cc_start: 0.8635 (m-80) cc_final: 0.8352 (m-80) REVERT: D 85 MET cc_start: 0.8994 (mtt) cc_final: 0.8582 (mtt) REVERT: D 154 GLN cc_start: 0.7998 (mm110) cc_final: 0.7731 (mt0) REVERT: E 150 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7352 (mpt-90) REVERT: E 154 GLN cc_start: 0.8006 (mm110) cc_final: 0.7698 (mt0) REVERT: E 373 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7448 (p0) REVERT: E 416 ASP cc_start: 0.7763 (t0) cc_final: 0.7499 (t0) outliers start: 70 outliers final: 48 residues processed: 226 average time/residue: 1.3235 time to fit residues: 347.3904 Evaluate side-chains 222 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 31 ILE 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 235 MET 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 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 438 VAL 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 222 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 285 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 C residue 31 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 163 ASP 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 235 MET 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 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 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 D residue 440 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 169 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 192 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.160313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110818 restraints weight = 30735.350| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.88 r_work: 0.3210 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2110 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= 0.117 Angle : 0.555 10.036 35118 Z= 0.289 Chirality : 0.045 0.171 3978 Planarity : 0.004 0.032 4476 Dihedral : 5.026 29.780 3426 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.06 % Favored : 93.75 % Rotamer: Outliers : 1.99 % Allowed : 17.75 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3168 helix: 1.51 (0.17), residues: 1044 sheet: -0.48 (0.19), residues: 666 loop : -1.34 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.006 0.001 HIS E 228 PHE 0.008 0.001 PHE D 225 TYR 0.016 0.001 TYR E 318 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 876) hydrogen bonds : angle 4.53703 ( 2502) covalent geometry : bond 0.00272 (25890) covalent geometry : angle 0.55548 (35118) ********************** 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 217 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 2.792 Fit side-chains revert: symmetry clash REVERT: F 145 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8044 (mm-30) REVERT: F 150 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.6797 (mpt-90) REVERT: F 154 GLN cc_start: 0.7958 (mm110) cc_final: 0.7698 (mt0) REVERT: F 163 ASP cc_start: 0.8402 (t70) cc_final: 0.8189 (t70) REVERT: F 281 LYS cc_start: 0.7423 (tttm) cc_final: 0.6990 (ptmt) REVERT: A 154 GLN cc_start: 0.7703 (mm110) cc_final: 0.7460 (mt0) REVERT: A 337 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8262 (mm) REVERT: A 365 GLU cc_start: 0.7800 (mp0) cc_final: 0.7454 (mp0) REVERT: B 154 GLN cc_start: 0.7791 (mm110) cc_final: 0.7526 (mt0) REVERT: B 337 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8309 (mm) REVERT: C 154 GLN cc_start: 0.7888 (mm110) cc_final: 0.7622 (mt0) REVERT: C 281 LYS cc_start: 0.7304 (tttm) cc_final: 0.6953 (ptmt) REVERT: C 347 TYR cc_start: 0.8658 (m-80) cc_final: 0.8331 (m-80) REVERT: D 85 MET cc_start: 0.8981 (mtt) cc_final: 0.8593 (mtt) REVERT: D 154 GLN cc_start: 0.7881 (mm110) cc_final: 0.7671 (mt0) REVERT: D 373 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7285 (p0) REVERT: E 150 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7412 (mpt-90) REVERT: E 154 GLN cc_start: 0.7926 (mm110) cc_final: 0.7640 (mt0) REVERT: E 365 GLU cc_start: 0.7807 (mp0) cc_final: 0.7573 (mp0) REVERT: E 373 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7381 (p0) REVERT: E 416 ASP cc_start: 0.7720 (t0) cc_final: 0.7465 (t0) outliers start: 55 outliers final: 41 residues processed: 209 average time/residue: 1.3916 time to fit residues: 337.4301 Evaluate side-chains 208 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 2.782 ------------------------------------------------------------------------------- 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 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 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 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 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 274 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 223 optimal weight: 0.0470 chunk 95 optimal weight: 6.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.155218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103864 restraints weight = 30261.872| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.89 r_work: 0.3098 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25890 Z= 0.178 Angle : 0.604 8.971 35118 Z= 0.317 Chirality : 0.048 0.194 3978 Planarity : 0.004 0.033 4476 Dihedral : 5.201 29.869 3426 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.67 % Favored : 92.14 % Rotamer: Outliers : 1.92 % Allowed : 17.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3168 helix: 1.38 (0.16), residues: 1044 sheet: -0.52 (0.19), residues: 666 loop : -1.41 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 230 HIS 0.007 0.001 HIS A 228 PHE 0.011 0.001 PHE D 225 TYR 0.018 0.002 TYR E 318 ARG 0.003 0.000 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 876) hydrogen bonds : angle 4.69755 ( 2502) covalent geometry : bond 0.00435 (25890) covalent geometry : angle 0.60414 (35118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18045.53 seconds wall clock time: 311 minutes 18.36 seconds (18678.36 seconds total)