Starting phenix.real_space_refine on Sat Jun 21 20:26:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hzx_35091/06_2025/8hzx_35091.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hzx_35091/06_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_35091/06_2025/8hzx_35091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hzx_35091/06_2025/8hzx_35091.map" model { file = "/net/cci-nas-00/data/ceres_data/8hzx_35091/06_2025/8hzx_35091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hzx_35091/06_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-5710/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: 11.04, per 1000 atoms: 0.44 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: 6.03 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: 3.33 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: 9.07 Time building geometry restraints manager: 7.19 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: 2.090 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: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 53.540 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.980 ------------------------------------------------------------------------------- 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 : 2.890 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: 1.6569 time to fit residues: 393.8674 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 : 2.600 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.160651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109823 restraints weight = 30615.960| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.91 r_work: 0.3189 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1008 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= 0.170 Angle : 0.593 6.399 35118 Z= 0.318 Chirality : 0.047 0.180 3978 Planarity : 0.004 0.031 4476 Dihedral : 5.260 27.271 3426 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.25 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 0.04854 ( 876) hydrogen bonds : angle 5.10350 ( 2502) covalent geometry : bond 0.00402 (25890) covalent geometry : angle 0.59257 (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 : 3.090 Fit side-chains revert: symmetry clash REVERT: F 58 MET cc_start: 0.8487 (mtm) cc_final: 0.8270 (mtm) REVERT: F 150 ARG cc_start: 0.8314 (mmt90) cc_final: 0.7893 (mtm-85) REVERT: F 154 GLN cc_start: 0.7966 (mm110) cc_final: 0.7583 (mt0) REVERT: F 163 ASP cc_start: 0.8319 (t70) cc_final: 0.8025 (t70) REVERT: F 281 LYS cc_start: 0.7290 (tttm) cc_final: 0.6953 (ptmt) REVERT: F 320 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6841 (ppp) REVERT: A 154 GLN cc_start: 0.7884 (mm110) cc_final: 0.7465 (mt0) REVERT: B 154 GLN cc_start: 0.7991 (mm110) cc_final: 0.7561 (mt0) REVERT: B 373 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7579 (p0) REVERT: C 58 MET cc_start: 0.8284 (mtm) cc_final: 0.7994 (mtt) REVERT: C 154 GLN cc_start: 0.7926 (mm110) cc_final: 0.7564 (mt0) REVERT: C 163 ASP cc_start: 0.8254 (t70) cc_final: 0.7961 (t70) REVERT: C 281 LYS cc_start: 0.7499 (tttm) cc_final: 0.7065 (ptmt) REVERT: C 347 TYR cc_start: 0.8626 (m-80) cc_final: 0.8404 (m-80) REVERT: C 428 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8428 (mptt) REVERT: D 85 MET cc_start: 0.8977 (mtt) cc_final: 0.8560 (mtt) REVERT: D 154 GLN cc_start: 0.8091 (mm110) cc_final: 0.7708 (mt0) REVERT: D 373 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7356 (p0) REVERT: E 85 MET cc_start: 0.8945 (mtt) cc_final: 0.8553 (mtt) REVERT: E 154 GLN cc_start: 0.8103 (mm110) cc_final: 0.7746 (mt0) REVERT: E 320 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6718 (ppp) REVERT: E 373 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7509 (p0) REVERT: E 416 ASP cc_start: 0.7860 (t0) cc_final: 0.7603 (t0) REVERT: E 428 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8352 (mmtt) outliers start: 95 outliers final: 31 residues processed: 253 average time/residue: 1.5103 time to fit residues: 441.7430 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 : 2.605 ------------------------------------------------------------------------------- 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: 0.0270 chunk 189 optimal weight: 0.7980 chunk 180 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.162778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112711 restraints weight = 30583.934| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.91 r_work: 0.3236 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25890 Z= 0.103 Angle : 0.521 9.502 35118 Z= 0.273 Chirality : 0.045 0.150 3978 Planarity : 0.004 0.029 4476 Dihedral : 4.897 27.565 3426 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.81 % Favored : 94.00 % Rotamer: Outliers : 2.46 % Allowed : 15.08 % Favored : 82.47 % 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: -0.46 (0.15), residues: 3168 helix: 0.85 (0.17), residues: 1086 sheet: -0.63 (0.19), residues: 660 loop : -0.98 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 290 HIS 0.006 0.001 HIS B 228 PHE 0.009 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 0.03781 ( 876) hydrogen bonds : angle 4.62733 ( 2502) covalent geometry : bond 0.00228 (25890) covalent geometry : angle 0.52070 (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 241 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 173 time to evaluate : 3.769 Fit side-chains REVERT: F 150 ARG cc_start: 0.8275 (mmt90) cc_final: 0.7909 (mtm-85) REVERT: F 154 GLN cc_start: 0.7841 (mm110) cc_final: 0.7471 (mt0) REVERT: F 163 ASP cc_start: 0.8340 (t70) cc_final: 0.8064 (t70) REVERT: F 281 LYS cc_start: 0.7265 (tttm) cc_final: 0.6833 (ptmt) REVERT: F 320 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6781 (ppp) REVERT: F 416 ASP cc_start: 0.7614 (t0) cc_final: 0.7376 (t70) REVERT: A 154 GLN cc_start: 0.7732 (mm110) cc_final: 0.7345 (mt0) REVERT: A 197 MET cc_start: 0.8498 (mmp) cc_final: 0.8105 (mmp) REVERT: A 260 GLN cc_start: 0.8137 (tt0) cc_final: 0.7885 (tt0) REVERT: B 154 GLN cc_start: 0.7874 (mm110) cc_final: 0.7487 (mt0) REVERT: B 260 GLN cc_start: 0.8045 (tt0) cc_final: 0.7766 (tt0) REVERT: B 425 ASP cc_start: 0.8140 (t0) cc_final: 0.7833 (t70) REVERT: C 58 MET cc_start: 0.8212 (mtm) cc_final: 0.7971 (mtt) REVERT: C 154 GLN cc_start: 0.7881 (mm110) cc_final: 0.7484 (mt0) REVERT: C 163 ASP cc_start: 0.8250 (t70) cc_final: 0.7956 (t70) REVERT: C 281 LYS cc_start: 0.7466 (tttm) cc_final: 0.6845 (ptmt) REVERT: C 347 TYR cc_start: 0.8619 (m-80) cc_final: 0.8341 (m-80) REVERT: C 362 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8095 (pt) REVERT: D 85 MET cc_start: 0.8958 (mtt) cc_final: 0.8515 (mtt) REVERT: D 154 GLN cc_start: 0.7947 (mm110) cc_final: 0.7650 (mt0) REVERT: D 373 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7340 (p0) REVERT: E 85 MET cc_start: 0.8938 (mtt) cc_final: 0.8500 (mtt) REVERT: E 154 GLN cc_start: 0.7950 (mm110) cc_final: 0.7631 (mt0) REVERT: E 416 ASP cc_start: 0.7689 (t0) cc_final: 0.7206 (t0) outliers start: 68 outliers final: 34 residues processed: 229 average time/residue: 1.5450 time to fit residues: 411.6676 Evaluate side-chains 200 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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 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 438 VAL 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 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 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 424 THR Chi-restraints excluded: chain E residue 438 VAL 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: 6.9990 chunk 312 optimal weight: 0.3980 chunk 227 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 E 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108824 restraints weight = 30811.339| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.90 r_work: 0.3174 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25890 Z= 0.176 Angle : 0.601 8.968 35118 Z= 0.320 Chirality : 0.048 0.190 3978 Planarity : 0.004 0.032 4476 Dihedral : 5.163 26.739 3426 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.34 % Favored : 93.47 % Rotamer: Outliers : 2.42 % Allowed : 15.26 % Favored : 82.32 % 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: -0.48 (0.15), residues: 3168 helix: 1.10 (0.16), residues: 1050 sheet: -0.58 (0.19), residues: 666 loop : -1.23 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 437 HIS 0.007 0.001 HIS A 228 PHE 0.013 0.002 PHE D 225 TYR 0.011 0.002 TYR C 318 ARG 0.003 0.000 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 876) hydrogen bonds : angle 4.78333 ( 2502) covalent geometry : bond 0.00424 (25890) covalent geometry : angle 0.60117 (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 232 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 165 time to evaluate : 3.580 Fit side-chains revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7930 (mm110) cc_final: 0.7574 (mt0) REVERT: F 163 ASP cc_start: 0.8381 (t70) cc_final: 0.8121 (t70) REVERT: F 281 LYS cc_start: 0.7365 (tttm) cc_final: 0.6974 (ptmt) REVERT: F 320 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6925 (ppp) REVERT: F 428 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8141 (mttm) REVERT: A 154 GLN cc_start: 0.7861 (mm110) cc_final: 0.7520 (mt0) REVERT: A 320 MET cc_start: 0.7203 (ppp) cc_final: 0.6801 (pmm) REVERT: A 322 GLU cc_start: 0.8550 (mp0) cc_final: 0.8302 (mp0) REVERT: A 337 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8282 (mm) REVERT: B 154 GLN cc_start: 0.7944 (mm110) cc_final: 0.7545 (mt0) REVERT: B 260 GLN cc_start: 0.8086 (tt0) cc_final: 0.7825 (tt0) REVERT: B 373 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7539 (p0) REVERT: B 425 ASP cc_start: 0.8120 (t0) cc_final: 0.7899 (t70) REVERT: C 154 GLN cc_start: 0.7946 (mm110) cc_final: 0.7557 (mt0) REVERT: C 163 ASP cc_start: 0.8334 (t70) cc_final: 0.8057 (t70) REVERT: C 322 GLU cc_start: 0.8610 (mp0) cc_final: 0.8260 (mp0) REVERT: D 85 MET cc_start: 0.8955 (mtt) cc_final: 0.8552 (mtt) REVERT: D 154 GLN cc_start: 0.8013 (mm110) cc_final: 0.7714 (mt0) REVERT: D 373 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7372 (p0) REVERT: E 85 MET cc_start: 0.8941 (mtt) cc_final: 0.8536 (mtt) REVERT: E 154 GLN cc_start: 0.7982 (mm110) cc_final: 0.7671 (mt0) REVERT: E 373 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7500 (p0) REVERT: E 416 ASP cc_start: 0.7826 (t0) cc_final: 0.7563 (t0) REVERT: E 428 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8369 (mmtt) outliers start: 67 outliers final: 39 residues processed: 223 average time/residue: 1.5664 time to fit residues: 404.5509 Evaluate side-chains 206 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 2.961 ------------------------------------------------------------------------------- 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 F residue 439 SER 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 362 ILE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 417 ASP 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 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 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 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: 6.9990 chunk 233 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109861 restraints weight = 30880.521| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.90 r_work: 0.3189 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25890 Z= 0.145 Angle : 0.561 8.222 35118 Z= 0.298 Chirality : 0.046 0.181 3978 Planarity : 0.004 0.031 4476 Dihedral : 5.098 27.885 3426 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.47 % Favored : 93.34 % Rotamer: Outliers : 2.49 % Allowed : 16.70 % Favored : 80.80 % 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: -0.40 (0.15), residues: 3168 helix: 1.05 (0.16), residues: 1080 sheet: -0.52 (0.19), residues: 666 loop : -1.13 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 230 HIS 0.007 0.001 HIS A 228 PHE 0.010 0.001 PHE D 225 TYR 0.012 0.001 TYR E 318 ARG 0.004 0.000 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 876) hydrogen bonds : angle 4.64898 ( 2502) covalent geometry : bond 0.00347 (25890) covalent geometry : angle 0.56086 (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 232 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 163 time to evaluate : 4.469 Fit side-chains revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7921 (mm110) cc_final: 0.7582 (mt0) REVERT: F 163 ASP cc_start: 0.8392 (t70) cc_final: 0.8131 (t70) REVERT: F 281 LYS cc_start: 0.7372 (tttm) cc_final: 0.6962 (ptmt) REVERT: A 154 GLN cc_start: 0.7811 (mm110) cc_final: 0.7486 (mt0) REVERT: A 320 MET cc_start: 0.7172 (ppp) cc_final: 0.6827 (pmm) REVERT: A 322 GLU cc_start: 0.8487 (mp0) cc_final: 0.8252 (mp0) REVERT: A 337 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8266 (mm) REVERT: B 154 GLN cc_start: 0.7897 (mm110) cc_final: 0.7599 (mt0) REVERT: B 260 GLN cc_start: 0.8058 (tt0) cc_final: 0.7798 (tt0) REVERT: B 337 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8323 (mm) REVERT: B 373 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7498 (p0) REVERT: B 425 ASP cc_start: 0.8111 (t0) cc_final: 0.7899 (t0) REVERT: C 154 GLN cc_start: 0.7919 (mm110) cc_final: 0.7545 (mt0) REVERT: C 163 ASP cc_start: 0.8332 (t70) cc_final: 0.8078 (t70) REVERT: C 281 LYS cc_start: 0.7355 (tttm) cc_final: 0.6971 (ptmt) REVERT: C 347 TYR cc_start: 0.8665 (m-80) cc_final: 0.8432 (m-80) REVERT: D 85 MET cc_start: 0.8959 (mtt) cc_final: 0.8530 (mtt) REVERT: D 154 GLN cc_start: 0.7965 (mm110) cc_final: 0.7715 (mt0) REVERT: D 373 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7348 (p0) REVERT: E 85 MET cc_start: 0.8910 (mtt) cc_final: 0.8539 (mtt) REVERT: E 154 GLN cc_start: 0.7959 (mm110) cc_final: 0.7662 (mt0) REVERT: E 373 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7466 (p0) REVERT: E 416 ASP cc_start: 0.7749 (t0) cc_final: 0.7467 (t0) REVERT: E 428 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8443 (mmtm) outliers start: 69 outliers final: 46 residues processed: 219 average time/residue: 1.9730 time to fit residues: 509.5628 Evaluate side-chains 211 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 2.710 ------------------------------------------------------------------------------- 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 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 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 373 ASP Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 186 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 269 optimal weight: 0.9980 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.160602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110718 restraints weight = 30704.656| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.90 r_work: 0.3207 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1797 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= 0.122 Angle : 0.540 9.916 35118 Z= 0.283 Chirality : 0.045 0.166 3978 Planarity : 0.004 0.032 4476 Dihedral : 4.950 28.010 3426 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.38 % Favored : 93.43 % Rotamer: Outliers : 2.57 % Allowed : 16.74 % Favored : 80.69 % 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: -0.27 (0.15), residues: 3168 helix: 1.41 (0.17), residues: 1044 sheet: -0.46 (0.19), residues: 666 loop : -1.21 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 230 HIS 0.006 0.001 HIS A 228 PHE 0.009 0.001 PHE D 225 TYR 0.012 0.001 TYR E 318 ARG 0.003 0.000 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 876) hydrogen bonds : angle 4.53105 ( 2502) covalent geometry : bond 0.00285 (25890) covalent geometry : angle 0.54027 (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 243 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7897 (mm110) cc_final: 0.7570 (mt0) REVERT: F 163 ASP cc_start: 0.8404 (t70) cc_final: 0.8142 (t70) REVERT: F 281 LYS cc_start: 0.7446 (tttm) cc_final: 0.7023 (ptmt) REVERT: F 322 GLU cc_start: 0.8410 (mp0) cc_final: 0.8139 (mp0) REVERT: A 154 GLN cc_start: 0.7702 (mm110) cc_final: 0.7394 (mt0) REVERT: A 337 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8261 (mm) REVERT: B 154 GLN cc_start: 0.7786 (mm110) cc_final: 0.7522 (mt0) REVERT: B 260 GLN cc_start: 0.8047 (tt0) cc_final: 0.7795 (tt0) REVERT: B 322 GLU cc_start: 0.8409 (mp0) cc_final: 0.8174 (mp0) REVERT: B 337 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 373 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7449 (p0) REVERT: B 425 ASP cc_start: 0.8043 (t0) cc_final: 0.7829 (t0) REVERT: C 58 MET cc_start: 0.8383 (mtm) cc_final: 0.8181 (ttm) REVERT: C 154 GLN cc_start: 0.7899 (mm110) cc_final: 0.7582 (mt0) REVERT: C 163 ASP cc_start: 0.8348 (t70) cc_final: 0.8086 (t70) REVERT: C 281 LYS cc_start: 0.7283 (tttm) cc_final: 0.6920 (ptmt) REVERT: D 85 MET cc_start: 0.8931 (mtt) cc_final: 0.8515 (mtt) REVERT: D 150 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7593 (mpt-90) REVERT: D 154 GLN cc_start: 0.7884 (mm110) cc_final: 0.7656 (mt0) REVERT: D 373 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7334 (p0) REVERT: E 85 MET cc_start: 0.8902 (mtt) cc_final: 0.8490 (mtt) REVERT: E 150 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7409 (mpt-90) REVERT: E 154 GLN cc_start: 0.7931 (mm110) cc_final: 0.7644 (mt0) REVERT: E 373 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7447 (p0) REVERT: E 416 ASP cc_start: 0.7730 (t0) cc_final: 0.7459 (t0) REVERT: E 428 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8364 (mmtt) outliers start: 71 outliers final: 45 residues processed: 232 average time/residue: 1.3763 time to fit residues: 371.2510 Evaluate side-chains 217 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 2.604 ------------------------------------------------------------------------------- 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 175 THR 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 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 373 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 D residue 150 ARG Chi-restraints excluded: chain D residue 163 ASP 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 D residue 461 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 238 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 186 optimal weight: 0.0470 chunk 312 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 313 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.160392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110545 restraints weight = 30895.272| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.90 r_work: 0.3200 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1867 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= 0.129 Angle : 0.550 9.514 35118 Z= 0.288 Chirality : 0.046 0.169 3978 Planarity : 0.004 0.031 4476 Dihedral : 4.954 27.868 3426 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.41 % Favored : 93.40 % Rotamer: Outliers : 2.82 % Allowed : 16.38 % Favored : 80.80 % 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: -0.26 (0.15), residues: 3168 helix: 1.43 (0.17), residues: 1044 sheet: -0.45 (0.19), residues: 666 loop : -1.22 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 230 HIS 0.006 0.001 HIS A 228 PHE 0.010 0.001 PHE D 225 TYR 0.013 0.001 TYR E 318 ARG 0.003 0.000 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 876) hydrogen bonds : angle 4.53415 ( 2502) covalent geometry : bond 0.00304 (25890) covalent geometry : angle 0.54980 (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 242 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 164 time to evaluate : 2.688 Fit side-chains revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7944 (mm110) cc_final: 0.7631 (mt0) REVERT: F 163 ASP cc_start: 0.8416 (t70) cc_final: 0.8157 (t70) REVERT: F 281 LYS cc_start: 0.7441 (tttm) cc_final: 0.6991 (ptmt) REVERT: F 322 GLU cc_start: 0.8386 (mp0) cc_final: 0.8158 (mp0) REVERT: F 335 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: A 154 GLN cc_start: 0.7697 (mm110) cc_final: 0.7420 (mt0) REVERT: B 154 GLN cc_start: 0.7792 (mm110) cc_final: 0.7534 (mt0) REVERT: B 260 GLN cc_start: 0.8059 (tt0) cc_final: 0.7808 (tt0) REVERT: B 337 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8301 (mm) REVERT: B 425 ASP cc_start: 0.8028 (t0) cc_final: 0.7799 (t0) REVERT: C 58 MET cc_start: 0.8363 (mtm) cc_final: 0.8155 (ttm) REVERT: C 92 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8418 (mtp) REVERT: C 154 GLN cc_start: 0.7940 (mm110) cc_final: 0.7642 (mt0) REVERT: C 163 ASP cc_start: 0.8347 (t70) cc_final: 0.8084 (t70) REVERT: C 281 LYS cc_start: 0.7264 (tttm) cc_final: 0.6932 (ptmt) REVERT: C 335 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: D 85 MET cc_start: 0.8947 (mtt) cc_final: 0.8563 (mtt) REVERT: D 150 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7775 (mpt-90) REVERT: D 154 GLN cc_start: 0.7872 (mm110) cc_final: 0.7648 (mt0) REVERT: D 373 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7321 (p0) REVERT: E 85 MET cc_start: 0.8921 (mtt) cc_final: 0.8534 (mtt) REVERT: E 150 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7410 (mpt-90) REVERT: E 154 GLN cc_start: 0.7918 (mm110) cc_final: 0.7627 (mt0) REVERT: E 373 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7403 (p0) REVERT: E 416 ASP cc_start: 0.7728 (t0) cc_final: 0.7453 (t0) REVERT: E 428 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8385 (mmtm) outliers start: 78 outliers final: 46 residues processed: 231 average time/residue: 1.3176 time to fit residues: 353.2588 Evaluate side-chains 215 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 2.643 ------------------------------------------------------------------------------- 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 335 GLU 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 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 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 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 92 MET 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 D residue 150 ARG Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 461 MET 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=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: 0.6980 chunk 177 optimal weight: 5.9990 chunk 112 optimal weight: 0.0570 chunk 275 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.159607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109750 restraints weight = 30669.007| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.89 r_work: 0.3190 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25890 Z= 0.145 Angle : 0.568 8.993 35118 Z= 0.298 Chirality : 0.046 0.180 3978 Planarity : 0.004 0.032 4476 Dihedral : 5.023 28.188 3426 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 2.68 % Allowed : 16.56 % Favored : 80.77 % 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: 1.43 (0.16), residues: 1044 sheet: -0.47 (0.19), residues: 666 loop : -1.27 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 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 F 150 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 876) hydrogen bonds : angle 4.58852 ( 2502) covalent geometry : bond 0.00348 (25890) covalent geometry : angle 0.56850 (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 235 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 161 time to evaluate : 3.658 Fit side-chains revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7956 (mm110) cc_final: 0.7660 (mt0) REVERT: F 163 ASP cc_start: 0.8389 (t70) cc_final: 0.8160 (t70) REVERT: F 281 LYS cc_start: 0.7439 (tttm) cc_final: 0.6969 (ptmt) REVERT: F 320 MET cc_start: 0.6883 (ppp) cc_final: 0.6592 (ppp) REVERT: A 154 GLN cc_start: 0.7732 (mm110) cc_final: 0.7452 (mt0) REVERT: A 337 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8257 (mm) REVERT: B 154 GLN cc_start: 0.7801 (mm110) cc_final: 0.7544 (mt0) REVERT: B 322 GLU cc_start: 0.8579 (mp0) cc_final: 0.8346 (mp0) REVERT: B 335 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: B 337 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8299 (mm) REVERT: B 425 ASP cc_start: 0.8058 (t0) cc_final: 0.7818 (t0) REVERT: C 58 MET cc_start: 0.8396 (mtm) cc_final: 0.8172 (ttm) REVERT: C 154 GLN cc_start: 0.7926 (mm110) cc_final: 0.7643 (mt0) REVERT: C 163 ASP cc_start: 0.8344 (t70) cc_final: 0.8097 (t70) REVERT: C 281 LYS cc_start: 0.7336 (tttm) cc_final: 0.6969 (ptmt) REVERT: C 335 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: C 347 TYR cc_start: 0.8657 (m-80) cc_final: 0.8390 (m-80) REVERT: D 85 MET cc_start: 0.8969 (mtt) cc_final: 0.8582 (mtt) REVERT: D 150 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7806 (mpt-90) REVERT: D 154 GLN cc_start: 0.7905 (mm110) cc_final: 0.7670 (mt0) REVERT: D 373 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7333 (p0) REVERT: E 150 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7431 (mpt-90) REVERT: E 154 GLN cc_start: 0.7950 (mm110) cc_final: 0.7667 (mt0) REVERT: E 373 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7397 (p0) REVERT: E 416 ASP cc_start: 0.7750 (t0) cc_final: 0.7488 (t0) REVERT: E 428 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8341 (mmtm) outliers start: 74 outliers final: 47 residues processed: 226 average time/residue: 1.6836 time to fit residues: 441.2876 Evaluate side-chains 216 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 2.672 ------------------------------------------------------------------------------- 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 175 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 MET 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 238 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 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 D residue 150 ARG Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 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: 0.9990 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 290 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.152476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098698 restraints weight = 30054.614| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.95 r_work: 0.3020 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 25890 Z= 0.286 Angle : 0.699 7.615 35118 Z= 0.372 Chirality : 0.053 0.226 3978 Planarity : 0.005 0.043 4476 Dihedral : 5.537 27.901 3426 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.55 % Rotamer: Outliers : 2.53 % Allowed : 16.52 % Favored : 80.95 % 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: -0.72 (0.14), residues: 3168 helix: 1.01 (0.16), residues: 1044 sheet: -0.62 (0.19), residues: 654 loop : -1.51 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 230 HIS 0.008 0.002 HIS C 228 PHE 0.016 0.002 PHE D 225 TYR 0.015 0.002 TYR E 318 ARG 0.004 0.001 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.05477 ( 876) hydrogen bonds : angle 5.01988 ( 2502) covalent geometry : bond 0.00704 (25890) covalent geometry : angle 0.69928 (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 240 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 170 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: F 31 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8231 (mm) REVERT: F 154 GLN cc_start: 0.7933 (mm110) cc_final: 0.7586 (mt0) REVERT: F 163 ASP cc_start: 0.8396 (t70) cc_final: 0.8191 (t70) REVERT: F 235 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8579 (mtm) REVERT: A 154 GLN cc_start: 0.7939 (mm110) cc_final: 0.7607 (mt0) REVERT: A 337 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8199 (mm) REVERT: A 365 GLU cc_start: 0.7997 (mp0) cc_final: 0.7635 (mp0) REVERT: B 154 GLN cc_start: 0.7923 (mm110) cc_final: 0.7625 (mt0) REVERT: B 337 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8237 (mm) REVERT: B 425 ASP cc_start: 0.8055 (t0) cc_final: 0.7808 (t0) REVERT: C 31 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8278 (mm) REVERT: C 154 GLN cc_start: 0.7908 (mm110) cc_final: 0.7548 (mt0) REVERT: C 163 ASP cc_start: 0.8323 (t70) cc_final: 0.8116 (t70) REVERT: C 235 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8565 (mtm) REVERT: D 85 MET cc_start: 0.8964 (mtt) cc_final: 0.8553 (mtt) REVERT: D 150 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7404 (mpt-90) REVERT: D 154 GLN cc_start: 0.8056 (mm110) cc_final: 0.7802 (mt0) REVERT: E 150 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7201 (mpt-90) REVERT: E 154 GLN cc_start: 0.8066 (mm110) cc_final: 0.7710 (mt0) REVERT: E 373 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7371 (p0) REVERT: E 416 ASP cc_start: 0.7749 (t70) cc_final: 0.7448 (t0) outliers start: 70 outliers final: 45 residues processed: 227 average time/residue: 1.4013 time to fit residues: 367.5898 Evaluate side-chains 218 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 2.658 ------------------------------------------------------------------------------- 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 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 175 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 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 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 31 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 235 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 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 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: 0.9990 chunk 268 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.156702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105595 restraints weight = 30355.784| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.90 r_work: 0.3124 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25890 Z= 0.120 Angle : 0.569 9.698 35118 Z= 0.297 Chirality : 0.046 0.175 3978 Planarity : 0.004 0.033 4476 Dihedral : 5.123 29.124 3426 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.34 % Favored : 93.47 % Rotamer: Outliers : 1.99 % Allowed : 17.28 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.15), residues: 3168 helix: 1.46 (0.17), residues: 1044 sheet: -0.55 (0.19), residues: 666 loop : -1.40 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.006 0.001 HIS B 228 PHE 0.008 0.001 PHE D 225 TYR 0.016 0.001 TYR E 318 ARG 0.002 0.000 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 876) hydrogen bonds : angle 4.59814 ( 2502) covalent geometry : bond 0.00276 (25890) covalent geometry : angle 0.56921 (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 222 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 4.228 Fit side-chains revert: symmetry clash REVERT: F 154 GLN cc_start: 0.7960 (mm110) cc_final: 0.7680 (mt0) REVERT: F 163 ASP cc_start: 0.8433 (t70) cc_final: 0.8218 (t70) REVERT: F 281 LYS cc_start: 0.7436 (tttm) cc_final: 0.6997 (ptmt) REVERT: A 154 GLN cc_start: 0.7739 (mm110) cc_final: 0.7481 (mt0) REVERT: A 337 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8288 (mm) REVERT: A 365 GLU cc_start: 0.7863 (mp0) cc_final: 0.7510 (mp0) REVERT: B 154 GLN cc_start: 0.7810 (mm110) cc_final: 0.7550 (mt0) REVERT: B 337 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8325 (mm) REVERT: C 154 GLN cc_start: 0.7881 (mm110) cc_final: 0.7577 (mt0) REVERT: C 163 ASP cc_start: 0.8371 (t70) cc_final: 0.8148 (t70) REVERT: C 281 LYS cc_start: 0.7360 (tttm) cc_final: 0.6993 (ptmt) REVERT: C 347 TYR cc_start: 0.8637 (m-80) cc_final: 0.8344 (m-80) REVERT: D 150 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7793 (mpt-90) REVERT: D 154 GLN cc_start: 0.7910 (mm110) cc_final: 0.7702 (mt0) REVERT: D 373 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7340 (p0) REVERT: E 150 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7437 (mpt-90) REVERT: E 154 GLN cc_start: 0.7919 (mm110) cc_final: 0.7642 (mt0) REVERT: E 365 GLU cc_start: 0.7733 (mp0) cc_final: 0.7517 (mp0) REVERT: E 373 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7444 (p0) REVERT: E 416 ASP cc_start: 0.7731 (t70) cc_final: 0.7433 (t0) outliers start: 55 outliers final: 42 residues processed: 214 average time/residue: 2.5756 time to fit residues: 648.0829 Evaluate side-chains 213 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 7.120 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain A residue 238 MET 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 274 optimal weight: 0.5980 chunk 307 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 223 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.161013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111622 restraints weight = 30718.572| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.90 r_work: 0.3220 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25890 Z= 0.110 Angle : 0.547 10.713 35118 Z= 0.282 Chirality : 0.045 0.159 3978 Planarity : 0.004 0.032 4476 Dihedral : 4.896 29.651 3426 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.44 % Favored : 93.37 % Rotamer: Outliers : 1.77 % Allowed : 17.61 % 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: -0.19 (0.15), residues: 3168 helix: 1.61 (0.17), residues: 1044 sheet: -0.36 (0.19), residues: 654 loop : -1.32 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 230 HIS 0.006 0.001 HIS A 228 PHE 0.008 0.001 PHE D 225 TYR 0.019 0.001 TYR D 318 ARG 0.002 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 876) hydrogen bonds : angle 4.44466 ( 2502) covalent geometry : bond 0.00255 (25890) covalent geometry : angle 0.54659 (35118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21091.95 seconds wall clock time: 375 minutes 49.29 seconds (22549.29 seconds total)