Starting phenix.real_space_refine on Tue Jan 21 19:39:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ezm_50089/01_2025/9ezm_50089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ezm_50089/01_2025/9ezm_50089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ezm_50089/01_2025/9ezm_50089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ezm_50089/01_2025/9ezm_50089.map" model { file = "/net/cci-nas-00/data/ceres_data/9ezm_50089/01_2025/9ezm_50089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ezm_50089/01_2025/9ezm_50089.cif" } resolution = 2.9 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= 0.007 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 162 5.16 5 C 42426 2.51 5 N 11574 2.21 5 O 13860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 378 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 68022 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3779 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 458} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 12.17, per 1000 atoms: 0.18 Number of scatterers: 68022 At special positions: 0 Unit cell: (276.1, 273.9, 110, 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 162 16.00 O 13860 8.00 N 11574 7.00 C 42426 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: 11.97 Conformation dependent library (CDL) restraints added in 6.6 seconds 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15804 Finding SS restraints... Secondary structure from input PDB file: 306 helices and 114 sheets defined 31.8% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.78 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.525A pdb=" N ASN A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY A 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 344 removed outlier: 3.867A pdb=" N SER A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 430 through 438 removed outlier: 3.500A pdb=" N ASP A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS A 468 " --> pdb=" O PRO A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG A 473 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.861A pdb=" N VAL A 491 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 517 Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.502A pdb=" N ALA A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 524 through 528' Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.525A pdb=" N ASN B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY B 117 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.553A pdb=" N TYR B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 344 removed outlier: 3.867A pdb=" N SER B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS B 468 " --> pdb=" O PRO B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 486 removed outlier: 3.798A pdb=" N ARG B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 491 removed outlier: 3.860A pdb=" N VAL B 491 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 517 Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.501A pdb=" N ALA B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 528' Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.526A pdb=" N ASN C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY C 117 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 313 removed outlier: 3.527A pdb=" N PHE C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 344 removed outlier: 3.867A pdb=" N SER C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP C 435 " --> pdb=" O LYS C 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 464 through 468 removed outlier: 3.982A pdb=" N LYS C 468 " --> pdb=" O PRO C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG C 473 " --> pdb=" O TYR C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 removed outlier: 3.861A pdb=" N VAL C 491 " --> pdb=" O GLN C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 517 Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.502A pdb=" N ALA C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 528' Processing helix chain 'C' and resid 539 through 545 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.525A pdb=" N ASN D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY D 117 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.866A pdb=" N SER D 335 " --> pdb=" O GLY D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 362 Processing helix chain 'D' and resid 393 through 408 Processing helix chain 'D' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS D 468 " --> pdb=" O PRO D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG D 473 " --> pdb=" O TYR D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 491 removed outlier: 3.861A pdb=" N VAL D 491 " --> pdb=" O GLN D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 517 Processing helix chain 'D' and resid 524 through 528 removed outlier: 3.503A pdb=" N ALA D 528 " --> pdb=" O SER D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 528' Processing helix chain 'D' and resid 539 through 545 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.526A pdb=" N ASN E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY E 117 " --> pdb=" O GLY E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 293 through 299 removed outlier: 3.555A pdb=" N TYR E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 313 removed outlier: 3.527A pdb=" N PHE E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 344 removed outlier: 3.868A pdb=" N SER E 335 " --> pdb=" O GLY E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 362 Processing helix chain 'E' and resid 393 through 408 Processing helix chain 'E' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP E 435 " --> pdb=" O LYS E 431 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL E 436 " --> pdb=" O GLY E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 441 No H-bonds generated for 'chain 'E' and resid 439 through 441' Processing helix chain 'E' and resid 464 through 468 removed outlier: 3.982A pdb=" N LYS E 468 " --> pdb=" O PRO E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG E 473 " --> pdb=" O TYR E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 491 removed outlier: 3.860A pdb=" N VAL E 491 " --> pdb=" O GLN E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 517 Processing helix chain 'E' and resid 524 through 528 removed outlier: 3.502A pdb=" N ALA E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 524 through 528' Processing helix chain 'E' and resid 539 through 545 Processing helix chain 'F' and resid 47 through 55 Processing helix chain 'F' and resid 63 through 74 removed outlier: 3.526A pdb=" N ASN F 74 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY F 117 " --> pdb=" O GLY F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 344 removed outlier: 3.866A pdb=" N SER F 335 " --> pdb=" O GLY F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 362 Processing helix chain 'F' and resid 393 through 408 Processing helix chain 'F' and resid 430 through 438 removed outlier: 3.500A pdb=" N ASP F 435 " --> pdb=" O LYS F 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL F 436 " --> pdb=" O GLY F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 441 No H-bonds generated for 'chain 'F' and resid 439 through 441' Processing helix chain 'F' and resid 464 through 468 removed outlier: 3.982A pdb=" N LYS F 468 " --> pdb=" O PRO F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG F 473 " --> pdb=" O TYR F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 491 removed outlier: 3.861A pdb=" N VAL F 491 " --> pdb=" O GLN F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 517 Processing helix chain 'F' and resid 524 through 528 removed outlier: 3.502A pdb=" N ALA F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 528' Processing helix chain 'F' and resid 539 through 545 Processing helix chain 'G' and resid 47 through 55 Processing helix chain 'G' and resid 63 through 74 removed outlier: 3.525A pdb=" N ASN G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY G 117 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 182 Processing helix chain 'G' and resid 293 through 299 removed outlier: 3.555A pdb=" N TYR G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 344 removed outlier: 3.866A pdb=" N SER G 335 " --> pdb=" O GLY G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 362 Processing helix chain 'G' and resid 393 through 408 Processing helix chain 'G' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP G 435 " --> pdb=" O LYS G 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL G 436 " --> pdb=" O GLY G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 441 No H-bonds generated for 'chain 'G' and resid 439 through 441' Processing helix chain 'G' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS G 468 " --> pdb=" O PRO G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 486 removed outlier: 3.798A pdb=" N ARG G 473 " --> pdb=" O TYR G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 491 removed outlier: 3.861A pdb=" N VAL G 491 " --> pdb=" O GLN G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 517 Processing helix chain 'G' and resid 524 through 528 removed outlier: 3.501A pdb=" N ALA G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 524 through 528' Processing helix chain 'G' and resid 539 through 545 Processing helix chain 'H' and resid 47 through 55 Processing helix chain 'H' and resid 63 through 74 removed outlier: 3.525A pdb=" N ASN H 74 " --> pdb=" O GLY H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY H 117 " --> pdb=" O GLY H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 182 Processing helix chain 'H' and resid 293 through 299 removed outlier: 3.552A pdb=" N TYR H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 313 removed outlier: 3.527A pdb=" N PHE H 312 " --> pdb=" O GLY H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 344 removed outlier: 3.868A pdb=" N SER H 335 " --> pdb=" O GLY H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 362 Processing helix chain 'H' and resid 393 through 408 Processing helix chain 'H' and resid 430 through 438 removed outlier: 3.502A pdb=" N ASP H 435 " --> pdb=" O LYS H 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL H 436 " --> pdb=" O GLY H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 441 No H-bonds generated for 'chain 'H' and resid 439 through 441' Processing helix chain 'H' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS H 468 " --> pdb=" O PRO H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 486 removed outlier: 3.798A pdb=" N ARG H 473 " --> pdb=" O TYR H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 491 removed outlier: 3.859A pdb=" N VAL H 491 " --> pdb=" O GLN H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 517 Processing helix chain 'H' and resid 524 through 528 removed outlier: 3.501A pdb=" N ALA H 528 " --> pdb=" O SER H 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 524 through 528' Processing helix chain 'H' and resid 539 through 545 Processing helix chain 'I' and resid 47 through 55 Processing helix chain 'I' and resid 63 through 74 removed outlier: 3.527A pdb=" N ASN I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY I 117 " --> pdb=" O GLY I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 182 Processing helix chain 'I' and resid 293 through 299 removed outlier: 3.555A pdb=" N TYR I 297 " --> pdb=" O THR I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 313 removed outlier: 3.527A pdb=" N PHE I 312 " --> pdb=" O GLY I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 344 removed outlier: 3.868A pdb=" N SER I 335 " --> pdb=" O GLY I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 362 Processing helix chain 'I' and resid 393 through 408 Processing helix chain 'I' and resid 430 through 438 removed outlier: 3.500A pdb=" N ASP I 435 " --> pdb=" O LYS I 431 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL I 436 " --> pdb=" O GLY I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 439 through 441 No H-bonds generated for 'chain 'I' and resid 439 through 441' Processing helix chain 'I' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS I 468 " --> pdb=" O PRO I 465 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 486 removed outlier: 3.800A pdb=" N ARG I 473 " --> pdb=" O TYR I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 491 removed outlier: 3.860A pdb=" N VAL I 491 " --> pdb=" O GLN I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 517 Processing helix chain 'I' and resid 524 through 528 removed outlier: 3.503A pdb=" N ALA I 528 " --> pdb=" O SER I 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 524 through 528' Processing helix chain 'I' and resid 539 through 545 Processing helix chain 'J' and resid 47 through 55 Processing helix chain 'J' and resid 63 through 74 removed outlier: 3.525A pdb=" N ASN J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY J 117 " --> pdb=" O GLY J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 182 Processing helix chain 'J' and resid 293 through 299 removed outlier: 3.553A pdb=" N TYR J 297 " --> pdb=" O THR J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE J 312 " --> pdb=" O GLY J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 344 removed outlier: 3.867A pdb=" N SER J 335 " --> pdb=" O GLY J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 362 Processing helix chain 'J' and resid 393 through 408 Processing helix chain 'J' and resid 430 through 438 removed outlier: 3.502A pdb=" N ASP J 435 " --> pdb=" O LYS J 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL J 436 " --> pdb=" O GLY J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 441 No H-bonds generated for 'chain 'J' and resid 439 through 441' Processing helix chain 'J' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS J 468 " --> pdb=" O PRO J 465 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG J 473 " --> pdb=" O TYR J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 491 removed outlier: 3.862A pdb=" N VAL J 491 " --> pdb=" O GLN J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 496 through 517 Processing helix chain 'J' and resid 524 through 528 removed outlier: 3.501A pdb=" N ALA J 528 " --> pdb=" O SER J 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 524 through 528' Processing helix chain 'J' and resid 539 through 545 Processing helix chain 'K' and resid 47 through 55 Processing helix chain 'K' and resid 63 through 74 removed outlier: 3.526A pdb=" N ASN K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY K 117 " --> pdb=" O GLY K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 182 Processing helix chain 'K' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR K 297 " --> pdb=" O THR K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 313 removed outlier: 3.527A pdb=" N PHE K 312 " --> pdb=" O GLY K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 344 removed outlier: 3.866A pdb=" N SER K 335 " --> pdb=" O GLY K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 362 Processing helix chain 'K' and resid 393 through 408 Processing helix chain 'K' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP K 435 " --> pdb=" O LYS K 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL K 436 " --> pdb=" O GLY K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 441 No H-bonds generated for 'chain 'K' and resid 439 through 441' Processing helix chain 'K' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS K 468 " --> pdb=" O PRO K 465 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG K 473 " --> pdb=" O TYR K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 491 removed outlier: 3.861A pdb=" N VAL K 491 " --> pdb=" O GLN K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 517 Processing helix chain 'K' and resid 524 through 528 removed outlier: 3.503A pdb=" N ALA K 528 " --> pdb=" O SER K 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 524 through 528' Processing helix chain 'K' and resid 539 through 545 Processing helix chain 'L' and resid 47 through 55 Processing helix chain 'L' and resid 63 through 74 removed outlier: 3.526A pdb=" N ASN L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY L 117 " --> pdb=" O GLY L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 182 Processing helix chain 'L' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR L 297 " --> pdb=" O THR L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE L 312 " --> pdb=" O GLY L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 344 removed outlier: 3.866A pdb=" N SER L 335 " --> pdb=" O GLY L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 362 Processing helix chain 'L' and resid 393 through 408 Processing helix chain 'L' and resid 430 through 438 removed outlier: 3.500A pdb=" N ASP L 435 " --> pdb=" O LYS L 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL L 436 " --> pdb=" O GLY L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 441 No H-bonds generated for 'chain 'L' and resid 439 through 441' Processing helix chain 'L' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS L 468 " --> pdb=" O PRO L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG L 473 " --> pdb=" O TYR L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 491 removed outlier: 3.860A pdb=" N VAL L 491 " --> pdb=" O GLN L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 496 through 517 Processing helix chain 'L' and resid 524 through 528 removed outlier: 3.501A pdb=" N ALA L 528 " --> pdb=" O SER L 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 524 through 528' Processing helix chain 'L' and resid 539 through 545 Processing helix chain 'M' and resid 47 through 55 Processing helix chain 'M' and resid 63 through 74 removed outlier: 3.526A pdb=" N ASN M 74 " --> pdb=" O GLY M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY M 117 " --> pdb=" O GLY M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 293 through 299 removed outlier: 3.555A pdb=" N TYR M 297 " --> pdb=" O THR M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 313 removed outlier: 3.527A pdb=" N PHE M 312 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing helix chain 'M' and resid 331 through 344 removed outlier: 3.867A pdb=" N SER M 335 " --> pdb=" O GLY M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 362 Processing helix chain 'M' and resid 393 through 408 Processing helix chain 'M' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP M 435 " --> pdb=" O LYS M 431 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL M 436 " --> pdb=" O GLY M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 441 No H-bonds generated for 'chain 'M' and resid 439 through 441' Processing helix chain 'M' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS M 468 " --> pdb=" O PRO M 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG M 473 " --> pdb=" O TYR M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 487 through 491 removed outlier: 3.860A pdb=" N VAL M 491 " --> pdb=" O GLN M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 496 through 517 Processing helix chain 'M' and resid 524 through 528 removed outlier: 3.503A pdb=" N ALA M 528 " --> pdb=" O SER M 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 524 through 528' Processing helix chain 'M' and resid 539 through 545 Processing helix chain 'N' and resid 47 through 55 Processing helix chain 'N' and resid 63 through 74 removed outlier: 3.525A pdb=" N ASN N 74 " --> pdb=" O GLY N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY N 117 " --> pdb=" O GLY N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 182 Processing helix chain 'N' and resid 293 through 299 removed outlier: 3.552A pdb=" N TYR N 297 " --> pdb=" O THR N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE N 312 " --> pdb=" O GLY N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 344 removed outlier: 3.867A pdb=" N SER N 335 " --> pdb=" O GLY N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 362 Processing helix chain 'N' and resid 393 through 408 Processing helix chain 'N' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP N 435 " --> pdb=" O LYS N 431 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL N 436 " --> pdb=" O GLY N 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 439 through 441 No H-bonds generated for 'chain 'N' and resid 439 through 441' Processing helix chain 'N' and resid 464 through 468 removed outlier: 3.980A pdb=" N LYS N 468 " --> pdb=" O PRO N 465 " (cutoff:3.500A) Processing helix chain 'N' and resid 469 through 486 removed outlier: 3.798A pdb=" N ARG N 473 " --> pdb=" O TYR N 469 " (cutoff:3.500A) Processing helix chain 'N' and resid 487 through 491 removed outlier: 3.859A pdb=" N VAL N 491 " --> pdb=" O GLN N 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 496 through 517 Processing helix chain 'N' and resid 524 through 528 removed outlier: 3.501A pdb=" N ALA N 528 " --> pdb=" O SER N 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 524 through 528' Processing helix chain 'N' and resid 539 through 545 Processing helix chain 'O' and resid 47 through 55 Processing helix chain 'O' and resid 63 through 74 removed outlier: 3.525A pdb=" N ASN O 74 " --> pdb=" O GLY O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY O 117 " --> pdb=" O GLY O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 182 Processing helix chain 'O' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR O 297 " --> pdb=" O THR O 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 313 removed outlier: 3.527A pdb=" N PHE O 312 " --> pdb=" O GLY O 308 " (cutoff:3.500A) Processing helix chain 'O' and resid 331 through 344 removed outlier: 3.866A pdb=" N SER O 335 " --> pdb=" O GLY O 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 362 Processing helix chain 'O' and resid 393 through 408 Processing helix chain 'O' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP O 435 " --> pdb=" O LYS O 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL O 436 " --> pdb=" O GLY O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 439 through 441 No H-bonds generated for 'chain 'O' and resid 439 through 441' Processing helix chain 'O' and resid 464 through 468 removed outlier: 3.982A pdb=" N LYS O 468 " --> pdb=" O PRO O 465 " (cutoff:3.500A) Processing helix chain 'O' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG O 473 " --> pdb=" O TYR O 469 " (cutoff:3.500A) Processing helix chain 'O' and resid 487 through 491 removed outlier: 3.860A pdb=" N VAL O 491 " --> pdb=" O GLN O 488 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 517 Processing helix chain 'O' and resid 524 through 528 removed outlier: 3.503A pdb=" N ALA O 528 " --> pdb=" O SER O 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 524 through 528' Processing helix chain 'O' and resid 539 through 545 Processing helix chain 'P' and resid 47 through 55 Processing helix chain 'P' and resid 63 through 74 removed outlier: 3.524A pdb=" N ASN P 74 " --> pdb=" O GLY P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY P 117 " --> pdb=" O GLY P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 182 Processing helix chain 'P' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR P 297 " --> pdb=" O THR P 293 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE P 312 " --> pdb=" O GLY P 308 " (cutoff:3.500A) Processing helix chain 'P' and resid 331 through 344 removed outlier: 3.866A pdb=" N SER P 335 " --> pdb=" O GLY P 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 358 through 362 Processing helix chain 'P' and resid 393 through 408 Processing helix chain 'P' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP P 435 " --> pdb=" O LYS P 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL P 436 " --> pdb=" O GLY P 432 " (cutoff:3.500A) Processing helix chain 'P' and resid 439 through 441 No H-bonds generated for 'chain 'P' and resid 439 through 441' Processing helix chain 'P' and resid 464 through 468 removed outlier: 3.982A pdb=" N LYS P 468 " --> pdb=" O PRO P 465 " (cutoff:3.500A) Processing helix chain 'P' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG P 473 " --> pdb=" O TYR P 469 " (cutoff:3.500A) Processing helix chain 'P' and resid 487 through 491 removed outlier: 3.861A pdb=" N VAL P 491 " --> pdb=" O GLN P 488 " (cutoff:3.500A) Processing helix chain 'P' and resid 496 through 517 Processing helix chain 'P' and resid 524 through 528 removed outlier: 3.502A pdb=" N ALA P 528 " --> pdb=" O SER P 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 524 through 528' Processing helix chain 'P' and resid 539 through 545 Processing helix chain 'Q' and resid 47 through 55 Processing helix chain 'Q' and resid 63 through 74 removed outlier: 3.526A pdb=" N ASN Q 74 " --> pdb=" O GLY Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY Q 117 " --> pdb=" O GLY Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 182 Processing helix chain 'Q' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR Q 297 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing helix chain 'Q' and resid 307 through 313 removed outlier: 3.527A pdb=" N PHE Q 312 " --> pdb=" O GLY Q 308 " (cutoff:3.500A) Processing helix chain 'Q' and resid 331 through 344 removed outlier: 3.867A pdb=" N SER Q 335 " --> pdb=" O GLY Q 331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 358 through 362 Processing helix chain 'Q' and resid 393 through 408 Processing helix chain 'Q' and resid 430 through 438 removed outlier: 3.501A pdb=" N ASP Q 435 " --> pdb=" O LYS Q 431 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL Q 436 " --> pdb=" O GLY Q 432 " (cutoff:3.500A) Processing helix chain 'Q' and resid 439 through 441 No H-bonds generated for 'chain 'Q' and resid 439 through 441' Processing helix chain 'Q' and resid 464 through 468 removed outlier: 3.981A pdb=" N LYS Q 468 " --> pdb=" O PRO Q 465 " (cutoff:3.500A) Processing helix chain 'Q' and resid 469 through 486 removed outlier: 3.799A pdb=" N ARG Q 473 " --> pdb=" O TYR Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 487 through 491 removed outlier: 3.861A pdb=" N VAL Q 491 " --> pdb=" O GLN Q 488 " (cutoff:3.500A) Processing helix chain 'Q' and resid 496 through 517 Processing helix chain 'Q' and resid 524 through 528 removed outlier: 3.503A pdb=" N ALA Q 528 " --> pdb=" O SER Q 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 524 through 528' Processing helix chain 'Q' and resid 539 through 545 Processing helix chain 'R' and resid 47 through 55 Processing helix chain 'R' and resid 63 through 74 removed outlier: 3.526A pdb=" N ASN R 74 " --> pdb=" O GLY R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 118 removed outlier: 3.636A pdb=" N GLY R 117 " --> pdb=" O GLY R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 182 Processing helix chain 'R' and resid 293 through 299 removed outlier: 3.554A pdb=" N TYR R 297 " --> pdb=" O THR R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 313 removed outlier: 3.526A pdb=" N PHE R 312 " --> pdb=" O GLY R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 344 removed outlier: 3.867A pdb=" N SER R 335 " --> pdb=" O GLY R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 362 Processing helix chain 'R' and resid 393 through 408 Processing helix chain 'R' and resid 430 through 438 removed outlier: 4.204A pdb=" N VAL R 436 " --> pdb=" O GLY R 432 " (cutoff:3.500A) Processing helix chain 'R' and resid 439 through 441 No H-bonds generated for 'chain 'R' and resid 439 through 441' Processing helix chain 'R' and resid 464 through 468 removed outlier: 3.982A pdb=" N LYS R 468 " --> pdb=" O PRO R 465 " (cutoff:3.500A) Processing helix chain 'R' and resid 469 through 486 removed outlier: 3.798A pdb=" N ARG R 473 " --> pdb=" O TYR R 469 " (cutoff:3.500A) Processing helix chain 'R' and resid 487 through 491 removed outlier: 3.862A pdb=" N VAL R 491 " --> pdb=" O GLN R 488 " (cutoff:3.500A) Processing helix chain 'R' and resid 496 through 517 Processing helix chain 'R' and resid 524 through 528 removed outlier: 3.502A pdb=" N ALA R 528 " --> pdb=" O SER R 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 524 through 528' Processing helix chain 'R' and resid 539 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY A 33 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A 28 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS A 322 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY A 30 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN A 443 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR A 373 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE A 445 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR A 375 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER A 447 " --> pdb=" O TYR A 375 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A 444 " --> pdb=" O TRP A 456 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 98 removed outlier: 6.618A pdb=" N GLY A 95 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU A 107 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 97 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY A 167 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 133 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY A 424 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 529 through 532 Processing sheet with id=AA8, first strand: chain 'B' and resid 8 through 13 removed outlier: 6.329A pdb=" N VAL A 563 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU B 12 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE A 565 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY B 33 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR B 28 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS B 322 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY B 30 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ASN B 443 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR B 373 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE B 445 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B 375 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER B 447 " --> pdb=" O TYR B 375 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS B 444 " --> pdb=" O TRP B 456 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 94 through 98 removed outlier: 6.619A pdb=" N GLY B 95 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU B 107 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU B 97 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 133 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AB4, first strand: chain 'B' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY B 424 " --> pdb=" O ASN B 379 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 529 through 532 Processing sheet with id=AB6, first strand: chain 'C' and resid 8 through 13 removed outlier: 6.341A pdb=" N VAL B 563 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU C 12 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE B 565 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 45 removed outlier: 3.616A pdb=" N GLY C 33 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C 28 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS C 322 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY C 30 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN C 443 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR C 373 " --> pdb=" O ASN C 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE C 445 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR C 375 " --> pdb=" O ILE C 445 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N SER C 447 " --> pdb=" O TYR C 375 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS C 444 " --> pdb=" O TRP C 456 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 94 through 98 removed outlier: 6.619A pdb=" N GLY C 95 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU C 107 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU C 97 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY C 167 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE C 133 " --> pdb=" O GLY C 167 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'C' and resid 388 through 391 removed outlier: 3.884A pdb=" N GLY C 424 " --> pdb=" O ASN C 379 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 529 through 532 Processing sheet with id=AC4, first strand: chain 'D' and resid 8 through 13 removed outlier: 6.347A pdb=" N VAL C 563 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLU D 12 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE C 565 " --> pdb=" O GLU D 12 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 43 through 45 removed outlier: 3.616A pdb=" N GLY D 33 " --> pdb=" O GLY D 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR D 28 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS D 322 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY D 30 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN D 443 " --> pdb=" O ALA D 371 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 373 " --> pdb=" O ASN D 443 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE D 445 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR D 375 " --> pdb=" O ILE D 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER D 447 " --> pdb=" O TYR D 375 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS D 444 " --> pdb=" O TRP D 456 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY D 95 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU D 107 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU D 97 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE D 133 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AC9, first strand: chain 'D' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY D 424 " --> pdb=" O ASN D 379 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 529 through 532 Processing sheet with id=AD2, first strand: chain 'E' and resid 8 through 13 removed outlier: 6.338A pdb=" N VAL D 563 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU E 12 " --> pdb=" O VAL D 563 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE D 565 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY E 33 " --> pdb=" O GLY E 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR E 28 " --> pdb=" O MET E 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS E 322 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY E 30 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ASN E 443 " --> pdb=" O ALA E 371 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR E 373 " --> pdb=" O ASN E 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE E 445 " --> pdb=" O TYR E 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR E 375 " --> pdb=" O ILE E 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER E 447 " --> pdb=" O TYR E 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS E 444 " --> pdb=" O TRP E 456 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY E 95 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU E 107 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU E 97 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY E 167 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE E 133 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AD7, first strand: chain 'E' and resid 388 through 391 removed outlier: 3.884A pdb=" N GLY E 424 " --> pdb=" O ASN E 379 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 529 through 532 Processing sheet with id=AD9, first strand: chain 'F' and resid 8 through 13 removed outlier: 6.334A pdb=" N VAL E 563 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLU F 12 " --> pdb=" O VAL E 563 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE E 565 " --> pdb=" O GLU F 12 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY F 33 " --> pdb=" O GLY F 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR F 28 " --> pdb=" O MET F 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS F 322 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY F 30 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN F 443 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR F 373 " --> pdb=" O ASN F 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE F 445 " --> pdb=" O TYR F 373 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR F 375 " --> pdb=" O ILE F 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER F 447 " --> pdb=" O TYR F 375 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS F 444 " --> pdb=" O TRP F 456 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY F 95 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU F 107 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU F 97 " --> pdb=" O ILE F 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE F 133 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 301 through 302 Processing sheet with id=AE5, first strand: chain 'F' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY F 424 " --> pdb=" O ASN F 379 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 529 through 532 Processing sheet with id=AE7, first strand: chain 'G' and resid 8 through 13 Processing sheet with id=AE8, first strand: chain 'G' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY G 33 " --> pdb=" O GLY G 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR G 28 " --> pdb=" O MET G 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS G 322 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY G 30 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ASN G 443 " --> pdb=" O ALA G 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR G 373 " --> pdb=" O ASN G 443 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE G 445 " --> pdb=" O TYR G 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR G 375 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N SER G 447 " --> pdb=" O TYR G 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS G 444 " --> pdb=" O TRP G 456 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 94 through 98 removed outlier: 6.618A pdb=" N GLY G 95 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU G 107 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU G 97 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE G 133 " --> pdb=" O GLY G 167 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AF3, first strand: chain 'G' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY G 424 " --> pdb=" O ASN G 379 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 8 through 13 removed outlier: 6.329A pdb=" N VAL G 563 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU H 12 " --> pdb=" O VAL G 563 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE G 565 " --> pdb=" O GLU H 12 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 43 through 45 removed outlier: 3.614A pdb=" N GLY H 33 " --> pdb=" O GLY H 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR H 28 " --> pdb=" O MET H 320 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS H 322 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY H 30 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N ASN H 443 " --> pdb=" O ALA H 371 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR H 373 " --> pdb=" O ASN H 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE H 445 " --> pdb=" O TYR H 373 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR H 375 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER H 447 " --> pdb=" O TYR H 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS H 444 " --> pdb=" O TRP H 456 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY H 95 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU H 107 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU H 97 " --> pdb=" O ILE H 105 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE H 133 " --> pdb=" O GLY H 167 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 301 through 302 Processing sheet with id=AF9, first strand: chain 'H' and resid 388 through 391 removed outlier: 3.884A pdb=" N GLY H 424 " --> pdb=" O ASN H 379 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 8 through 13 removed outlier: 6.341A pdb=" N VAL H 563 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU I 12 " --> pdb=" O VAL H 563 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE H 565 " --> pdb=" O GLU I 12 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 43 through 45 removed outlier: 3.616A pdb=" N GLY I 33 " --> pdb=" O GLY I 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR I 28 " --> pdb=" O MET I 320 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS I 322 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY I 30 " --> pdb=" O CYS I 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN I 443 " --> pdb=" O ALA I 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR I 373 " --> pdb=" O ASN I 443 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE I 445 " --> pdb=" O TYR I 373 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR I 375 " --> pdb=" O ILE I 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER I 447 " --> pdb=" O TYR I 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS I 444 " --> pdb=" O TRP I 456 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 94 through 98 removed outlier: 6.619A pdb=" N GLY I 95 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU I 107 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU I 97 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE I 133 " --> pdb=" O GLY I 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AG6, first strand: chain 'I' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY I 424 " --> pdb=" O ASN I 379 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 8 through 13 removed outlier: 6.347A pdb=" N VAL I 563 " --> pdb=" O TYR J 10 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU J 12 " --> pdb=" O VAL I 563 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE I 565 " --> pdb=" O GLU J 12 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY J 33 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR J 28 " --> pdb=" O MET J 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS J 322 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY J 30 " --> pdb=" O CYS J 322 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ASN J 443 " --> pdb=" O ALA J 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR J 373 " --> pdb=" O ASN J 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE J 445 " --> pdb=" O TYR J 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR J 375 " --> pdb=" O ILE J 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER J 447 " --> pdb=" O TYR J 375 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS J 444 " --> pdb=" O TRP J 456 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 94 through 98 removed outlier: 6.619A pdb=" N GLY J 95 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU J 107 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU J 97 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY J 167 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE J 133 " --> pdb=" O GLY J 167 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 301 through 302 Processing sheet with id=AH3, first strand: chain 'J' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY J 424 " --> pdb=" O ASN J 379 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 8 through 13 removed outlier: 6.339A pdb=" N VAL J 563 " --> pdb=" O TYR K 10 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU K 12 " --> pdb=" O VAL J 563 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE J 565 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY K 33 " --> pdb=" O GLY K 82 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR K 28 " --> pdb=" O MET K 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS K 322 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY K 30 " --> pdb=" O CYS K 322 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N ASN K 443 " --> pdb=" O ALA K 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR K 373 " --> pdb=" O ASN K 443 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE K 445 " --> pdb=" O TYR K 373 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR K 375 " --> pdb=" O ILE K 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER K 447 " --> pdb=" O TYR K 375 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS K 444 " --> pdb=" O TRP K 456 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY K 95 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU K 107 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU K 97 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY K 167 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE K 133 " --> pdb=" O GLY K 167 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 301 through 302 Processing sheet with id=AH9, first strand: chain 'K' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY K 424 " --> pdb=" O ASN K 379 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.333A pdb=" N VAL K 563 " --> pdb=" O TYR L 10 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU L 12 " --> pdb=" O VAL K 563 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE K 565 " --> pdb=" O GLU L 12 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 43 through 45 removed outlier: 3.616A pdb=" N GLY L 33 " --> pdb=" O GLY L 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR L 28 " --> pdb=" O MET L 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS L 322 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY L 30 " --> pdb=" O CYS L 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN L 443 " --> pdb=" O ALA L 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR L 373 " --> pdb=" O ASN L 443 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE L 445 " --> pdb=" O TYR L 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR L 375 " --> pdb=" O ILE L 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER L 447 " --> pdb=" O TYR L 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS L 444 " --> pdb=" O TRP L 456 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY L 95 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU L 107 " --> pdb=" O GLY L 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU L 97 " --> pdb=" O ILE L 105 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY L 167 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE L 133 " --> pdb=" O GLY L 167 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 301 through 302 Processing sheet with id=AI6, first strand: chain 'L' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY L 424 " --> pdb=" O ASN L 379 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 8 through 13 Processing sheet with id=AI8, first strand: chain 'M' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY M 33 " --> pdb=" O GLY M 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR M 28 " --> pdb=" O MET M 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS M 322 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY M 30 " --> pdb=" O CYS M 322 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N ASN M 443 " --> pdb=" O ALA M 371 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR M 373 " --> pdb=" O ASN M 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE M 445 " --> pdb=" O TYR M 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR M 375 " --> pdb=" O ILE M 445 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N SER M 447 " --> pdb=" O TYR M 375 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS M 444 " --> pdb=" O TRP M 456 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'M' and resid 94 through 98 removed outlier: 6.618A pdb=" N GLY M 95 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU M 107 " --> pdb=" O GLY M 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU M 97 " --> pdb=" O ILE M 105 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'M' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY M 167 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE M 133 " --> pdb=" O GLY M 167 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'M' and resid 301 through 302 Processing sheet with id=AJ3, first strand: chain 'M' and resid 388 through 391 removed outlier: 3.884A pdb=" N GLY M 424 " --> pdb=" O ASN M 379 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'M' and resid 562 through 567 removed outlier: 6.328A pdb=" N VAL M 563 " --> pdb=" O TYR N 10 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU N 12 " --> pdb=" O VAL M 563 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE M 565 " --> pdb=" O GLU N 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'N' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY N 33 " --> pdb=" O GLY N 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR N 28 " --> pdb=" O MET N 320 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS N 322 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY N 30 " --> pdb=" O CYS N 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN N 443 " --> pdb=" O ALA N 371 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR N 373 " --> pdb=" O ASN N 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE N 445 " --> pdb=" O TYR N 373 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR N 375 " --> pdb=" O ILE N 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER N 447 " --> pdb=" O TYR N 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS N 444 " --> pdb=" O TRP N 456 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'N' and resid 94 through 98 removed outlier: 6.619A pdb=" N GLY N 95 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU N 107 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU N 97 " --> pdb=" O ILE N 105 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'N' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY N 167 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE N 133 " --> pdb=" O GLY N 167 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N' and resid 301 through 302 Processing sheet with id=AJ9, first strand: chain 'N' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY N 424 " --> pdb=" O ASN N 379 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'N' and resid 562 through 567 removed outlier: 6.341A pdb=" N VAL N 563 " --> pdb=" O TYR O 10 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU O 12 " --> pdb=" O VAL N 563 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE N 565 " --> pdb=" O GLU O 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'O' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY O 33 " --> pdb=" O GLY O 82 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR O 28 " --> pdb=" O MET O 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS O 322 " --> pdb=" O THR O 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY O 30 " --> pdb=" O CYS O 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN O 443 " --> pdb=" O ALA O 371 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR O 373 " --> pdb=" O ASN O 443 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE O 445 " --> pdb=" O TYR O 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR O 375 " --> pdb=" O ILE O 445 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N SER O 447 " --> pdb=" O TYR O 375 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS O 444 " --> pdb=" O TRP O 456 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 94 through 98 removed outlier: 6.618A pdb=" N GLY O 95 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU O 107 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU O 97 " --> pdb=" O ILE O 105 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 161 through 168 removed outlier: 4.689A pdb=" N GLY O 167 " --> pdb=" O PHE O 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE O 133 " --> pdb=" O GLY O 167 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'O' and resid 301 through 302 Processing sheet with id=AK6, first strand: chain 'O' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY O 424 " --> pdb=" O ASN O 379 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'O' and resid 562 through 567 removed outlier: 6.347A pdb=" N VAL O 563 " --> pdb=" O TYR P 10 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU P 12 " --> pdb=" O VAL O 563 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE O 565 " --> pdb=" O GLU P 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK7 Processing sheet with id=AK8, first strand: chain 'P' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY P 33 " --> pdb=" O GLY P 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR P 28 " --> pdb=" O MET P 320 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS P 322 " --> pdb=" O THR P 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY P 30 " --> pdb=" O CYS P 322 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ASN P 443 " --> pdb=" O ALA P 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR P 373 " --> pdb=" O ASN P 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE P 445 " --> pdb=" O TYR P 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR P 375 " --> pdb=" O ILE P 445 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N SER P 447 " --> pdb=" O TYR P 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS P 444 " --> pdb=" O TRP P 456 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'P' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY P 95 " --> pdb=" O GLU P 107 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU P 107 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU P 97 " --> pdb=" O ILE P 105 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'P' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY P 167 " --> pdb=" O PHE P 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE P 133 " --> pdb=" O GLY P 167 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'P' and resid 301 through 302 Processing sheet with id=AL3, first strand: chain 'P' and resid 388 through 391 removed outlier: 3.882A pdb=" N GLY P 424 " --> pdb=" O ASN P 379 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'P' and resid 562 through 567 removed outlier: 6.339A pdb=" N VAL P 563 " --> pdb=" O TYR Q 10 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU Q 12 " --> pdb=" O VAL P 563 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE P 565 " --> pdb=" O GLU Q 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'Q' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY Q 33 " --> pdb=" O GLY Q 82 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR Q 28 " --> pdb=" O MET Q 320 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS Q 322 " --> pdb=" O THR Q 28 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY Q 30 " --> pdb=" O CYS Q 322 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ASN Q 443 " --> pdb=" O ALA Q 371 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR Q 373 " --> pdb=" O ASN Q 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE Q 445 " --> pdb=" O TYR Q 373 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR Q 375 " --> pdb=" O ILE Q 445 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N SER Q 447 " --> pdb=" O TYR Q 375 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS Q 444 " --> pdb=" O TRP Q 456 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'Q' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY Q 95 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU Q 107 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU Q 97 " --> pdb=" O ILE Q 105 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'Q' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY Q 167 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE Q 133 " --> pdb=" O GLY Q 167 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'Q' and resid 301 through 302 Processing sheet with id=AL9, first strand: chain 'Q' and resid 388 through 391 removed outlier: 3.883A pdb=" N GLY Q 424 " --> pdb=" O ASN Q 379 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Q' and resid 562 through 567 removed outlier: 6.333A pdb=" N VAL Q 563 " --> pdb=" O TYR R 10 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU R 12 " --> pdb=" O VAL Q 563 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE Q 565 " --> pdb=" O GLU R 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM1 Processing sheet with id=AM2, first strand: chain 'R' and resid 43 through 45 removed outlier: 3.615A pdb=" N GLY R 33 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR R 28 " --> pdb=" O MET R 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS R 322 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY R 30 " --> pdb=" O CYS R 322 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ASN R 443 " --> pdb=" O ALA R 371 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR R 373 " --> pdb=" O ASN R 443 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE R 445 " --> pdb=" O TYR R 373 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR R 375 " --> pdb=" O ILE R 445 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N SER R 447 " --> pdb=" O TYR R 375 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS R 444 " --> pdb=" O TRP R 456 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'R' and resid 94 through 98 removed outlier: 6.620A pdb=" N GLY R 95 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU R 107 " --> pdb=" O GLY R 95 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU R 97 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'R' and resid 161 through 168 removed outlier: 4.688A pdb=" N GLY R 167 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE R 133 " --> pdb=" O GLY R 167 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'R' and resid 301 through 302 Processing sheet with id=AM6, first strand: chain 'R' and resid 388 through 391 removed outlier: 3.884A pdb=" N GLY R 424 " --> pdb=" O ASN R 379 " (cutoff:3.500A) 2458 hydrogen bonds defined for protein. 6762 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: 36.08 Time building geometry restraints manager: 14.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23411 1.34 - 1.45: 9204 1.45 - 1.57: 36703 1.57 - 1.69: 0 1.69 - 1.80: 234 Bond restraints: 69552 Sorted by residual: bond pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " ideal model delta sigma weight residual 1.808 1.777 0.031 3.30e-02 9.18e+02 8.71e-01 bond pdb=" CB CYS L 79 " pdb=" SG CYS L 79 " ideal model delta sigma weight residual 1.808 1.777 0.031 3.30e-02 9.18e+02 8.66e-01 bond pdb=" CB CYS N 79 " pdb=" SG CYS N 79 " ideal model delta sigma weight residual 1.808 1.777 0.031 3.30e-02 9.18e+02 8.56e-01 bond pdb=" CB CYS B 79 " pdb=" SG CYS B 79 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.44e-01 bond pdb=" CB CYS P 79 " pdb=" SG CYS P 79 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.42e-01 ... (remaining 69547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 94184 3.15 - 6.30: 388 6.30 - 9.44: 36 9.44 - 12.59: 0 12.59 - 15.74: 18 Bond angle restraints: 94626 Sorted by residual: angle pdb=" CA LEU K 470 " pdb=" CB LEU K 470 " pdb=" CG LEU K 470 " ideal model delta sigma weight residual 116.30 132.04 -15.74 3.50e+00 8.16e-02 2.02e+01 angle pdb=" CA LEU Q 470 " pdb=" CB LEU Q 470 " pdb=" CG LEU Q 470 " ideal model delta sigma weight residual 116.30 132.04 -15.74 3.50e+00 8.16e-02 2.02e+01 angle pdb=" CA LEU I 470 " pdb=" CB LEU I 470 " pdb=" CG LEU I 470 " ideal model delta sigma weight residual 116.30 132.03 -15.73 3.50e+00 8.16e-02 2.02e+01 angle pdb=" CA LEU M 470 " pdb=" CB LEU M 470 " pdb=" CG LEU M 470 " ideal model delta sigma weight residual 116.30 132.02 -15.72 3.50e+00 8.16e-02 2.02e+01 angle pdb=" CA LEU J 470 " pdb=" CB LEU J 470 " pdb=" CG LEU J 470 " ideal model delta sigma weight residual 116.30 132.02 -15.72 3.50e+00 8.16e-02 2.02e+01 ... (remaining 94621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 37242 17.53 - 35.06: 3420 35.06 - 52.59: 504 52.59 - 70.11: 36 70.11 - 87.64: 54 Dihedral angle restraints: 41256 sinusoidal: 16416 harmonic: 24840 Sorted by residual: dihedral pdb=" CA GLU M 496 " pdb=" C GLU M 496 " pdb=" N GLN M 497 " pdb=" CA GLN M 497 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLU R 496 " pdb=" C GLU R 496 " pdb=" N GLN R 497 " pdb=" CA GLN R 497 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLU Q 496 " pdb=" C GLU Q 496 " pdb=" N GLN Q 497 " pdb=" CA GLN Q 497 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 41253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 5087 0.031 - 0.062: 3194 0.062 - 0.094: 920 0.094 - 0.125: 730 0.125 - 0.156: 167 Chirality restraints: 10098 Sorted by residual: chirality pdb=" CA VAL M 550 " pdb=" N VAL M 550 " pdb=" C VAL M 550 " pdb=" CB VAL M 550 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA VAL G 550 " pdb=" N VAL G 550 " pdb=" C VAL G 550 " pdb=" CB VAL G 550 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA VAL D 550 " pdb=" N VAL D 550 " pdb=" C VAL D 550 " pdb=" CB VAL D 550 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 10095 not shown) Planarity restraints: 12816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO J 392 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO J 393 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO J 393 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 393 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 392 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO N 393 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO N 393 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO N 393 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 392 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 393 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 393 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 393 " -0.026 5.00e-02 4.00e+02 ... (remaining 12813 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 344 2.62 - 3.19: 53771 3.19 - 3.76: 94070 3.76 - 4.33: 144181 4.33 - 4.90: 237838 Nonbonded interactions: 530204 Sorted by model distance: nonbonded pdb=" CE2 TYR J 129 " pdb=" NE ARG P 387 " model vdw 2.054 3.420 nonbonded pdb=" CE2 TYR I 129 " pdb=" NE ARG O 387 " model vdw 2.056 3.420 nonbonded pdb=" CE2 TYR K 129 " pdb=" NE ARG Q 387 " model vdw 2.058 3.420 nonbonded pdb=" CE2 TYR L 129 " pdb=" NE ARG R 387 " model vdw 2.059 3.420 nonbonded pdb=" CE2 TYR G 129 " pdb=" NE ARG M 387 " model vdw 2.059 3.420 ... (remaining 530199 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: 0.45 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'R' } 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: 7.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.950 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 109.810 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.004 0.032 69552 Z= 0.282 Angle : 0.693 15.738 94626 Z= 0.383 Chirality : 0.050 0.156 10098 Planarity : 0.005 0.048 12816 Dihedral : 13.383 87.642 25452 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.94 (0.08), residues: 8694 helix: -0.94 (0.10), residues: 2160 sheet: -0.25 (0.11), residues: 1674 loop : -1.88 (0.07), residues: 4860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 204 HIS 0.006 0.002 HIS N 339 PHE 0.011 0.002 PHE N 478 TYR 0.016 0.002 TYR O 401 ARG 0.004 0.000 ARG K 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1326 time to evaluate : 5.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8169 (mt0) cc_final: 0.7967 (tt0) REVERT: A 183 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 306 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8006 (mtp85) REVERT: A 317 GLU cc_start: 0.7594 (mp0) cc_final: 0.7385 (mp0) REVERT: A 363 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7195 (tp30) REVERT: A 386 ASN cc_start: 0.8001 (m-40) cc_final: 0.7745 (m-40) REVERT: C 189 ASP cc_start: 0.7387 (m-30) cc_final: 0.7076 (m-30) REVERT: C 363 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7271 (tp30) REVERT: C 386 ASN cc_start: 0.7966 (m-40) cc_final: 0.7765 (m-40) REVERT: C 435 ASP cc_start: 0.7760 (m-30) cc_final: 0.7518 (m-30) REVERT: D 15 GLN cc_start: 0.8164 (mt0) cc_final: 0.7926 (tt0) REVERT: D 306 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7951 (mtp85) REVERT: D 363 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7154 (tp30) REVERT: D 386 ASN cc_start: 0.8118 (m-40) cc_final: 0.7805 (m-40) REVERT: F 189 ASP cc_start: 0.7466 (m-30) cc_final: 0.7139 (m-30) REVERT: F 363 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7349 (tp30) REVERT: F 435 ASP cc_start: 0.7715 (m-30) cc_final: 0.7479 (m-30) REVERT: G 171 ASP cc_start: 0.7071 (t0) cc_final: 0.6838 (t0) REVERT: G 480 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7965 (mt-10) REVERT: G 485 GLU cc_start: 0.7256 (mt-10) cc_final: 0.7011 (mt-10) REVERT: H 115 GLN cc_start: 0.7714 (tt0) cc_final: 0.7465 (tt0) REVERT: H 306 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7861 (mmt180) REVERT: H 362 MET cc_start: 0.8782 (mtp) cc_final: 0.8582 (mtp) REVERT: H 480 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7826 (mt-10) REVERT: H 536 GLU cc_start: 0.8074 (pm20) cc_final: 0.7442 (mp0) REVERT: I 26 THR cc_start: 0.8236 (p) cc_final: 0.8008 (p) REVERT: I 160 ASP cc_start: 0.7277 (m-30) cc_final: 0.6945 (m-30) REVERT: I 363 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7184 (tp30) REVERT: J 171 ASP cc_start: 0.7073 (t0) cc_final: 0.6828 (t0) REVERT: J 480 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7994 (mt-10) REVERT: J 485 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7038 (mt-10) REVERT: K 115 GLN cc_start: 0.7727 (tt0) cc_final: 0.7481 (tt0) REVERT: K 306 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7868 (mmt180) REVERT: K 362 MET cc_start: 0.8769 (mtp) cc_final: 0.8532 (mtp) REVERT: K 480 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7798 (mt-10) REVERT: K 536 GLU cc_start: 0.8134 (pm20) cc_final: 0.7452 (mp0) REVERT: L 115 GLN cc_start: 0.7769 (tt0) cc_final: 0.7520 (tt0) REVERT: L 160 ASP cc_start: 0.7356 (m-30) cc_final: 0.7003 (m-30) REVERT: L 330 ASP cc_start: 0.7160 (p0) cc_final: 0.6958 (p0) REVERT: L 363 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7017 (tp30) REVERT: L 480 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7939 (mt-10) REVERT: M 15 GLN cc_start: 0.8467 (mt0) cc_final: 0.7952 (tt0) REVERT: M 343 MET cc_start: 0.8765 (mmm) cc_final: 0.8564 (mmp) REVERT: N 194 ASP cc_start: 0.6971 (t0) cc_final: 0.6724 (m-30) REVERT: N 343 MET cc_start: 0.8764 (mmm) cc_final: 0.8516 (mmp) REVERT: O 22 GLU cc_start: 0.7364 (tt0) cc_final: 0.7105 (tt0) REVERT: O 26 THR cc_start: 0.8263 (p) cc_final: 0.8003 (t) REVERT: P 15 GLN cc_start: 0.8444 (mt0) cc_final: 0.7947 (tt0) REVERT: P 343 MET cc_start: 0.8786 (mmm) cc_final: 0.8567 (mmp) REVERT: Q 194 ASP cc_start: 0.6956 (t0) cc_final: 0.6700 (m-30) REVERT: R 22 GLU cc_start: 0.7405 (tt0) cc_final: 0.7169 (tt0) REVERT: R 194 ASP cc_start: 0.6955 (t0) cc_final: 0.6702 (m-30) outliers start: 0 outliers final: 2 residues processed: 1326 average time/residue: 1.5275 time to fit residues: 2604.5448 Evaluate side-chains 912 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 910 time to evaluate : 5.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain K residue 104 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 729 optimal weight: 10.0000 chunk 654 optimal weight: 5.9990 chunk 363 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 441 optimal weight: 30.0000 chunk 349 optimal weight: 8.9990 chunk 677 optimal weight: 0.0470 chunk 262 optimal weight: 8.9990 chunk 411 optimal weight: 8.9990 chunk 504 optimal weight: 7.9990 chunk 784 optimal weight: 30.0000 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 111 ASN A 151 HIS A 408 HIS B 47 ASN B 111 ASN B 408 HIS C 47 ASN C 111 ASN C 115 GLN C 408 HIS C 471 ASN D 47 ASN D 111 ASN D 408 HIS E 47 ASN E 111 ASN E 131 ASN E 408 HIS F 111 ASN F 115 GLN F 151 HIS F 408 HIS F 471 ASN G 15 GLN G 47 ASN G 131 ASN G 408 HIS H 15 GLN H 47 ASN H 408 HIS I 47 ASN I 355 ASN I 408 HIS I 427 HIS I 428 ASN J 15 GLN J 47 ASN J 408 HIS K 47 ASN K 408 HIS L 47 ASN L 355 ASN L 408 HIS L 427 HIS M 47 ASN M 355 ASN M 408 HIS N 408 HIS N 471 ASN O 47 ASN O 111 ASN O 408 HIS P 408 HIS Q 47 ASN Q 408 HIS Q 471 ASN R 47 ASN R 408 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.101032 restraints weight = 76752.132| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.17 r_work: 0.2807 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 69552 Z= 0.305 Angle : 0.658 16.954 94626 Z= 0.345 Chirality : 0.051 0.184 10098 Planarity : 0.005 0.068 12816 Dihedral : 5.302 140.323 9492 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.89 % Allowed : 11.82 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.05 (0.08), residues: 8694 helix: 0.04 (0.10), residues: 2304 sheet: 0.53 (0.12), residues: 1548 loop : -1.53 (0.08), residues: 4842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 204 HIS 0.007 0.002 HIS Q 339 PHE 0.012 0.002 PHE P 347 TYR 0.017 0.002 TYR J 401 ARG 0.004 0.001 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 883 time to evaluate : 5.974 Fit side-chains REVERT: A 15 GLN cc_start: 0.8572 (mt0) cc_final: 0.8197 (tt0) REVERT: A 107 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: A 111 ASN cc_start: 0.8468 (t0) cc_final: 0.8262 (t0) REVERT: A 162 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7662 (tp30) REVERT: A 306 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8165 (mtp85) REVERT: A 363 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7713 (tp30) REVERT: A 386 ASN cc_start: 0.8075 (m-40) cc_final: 0.7780 (m110) REVERT: B 191 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: B 362 MET cc_start: 0.9026 (mtp) cc_final: 0.8754 (mtp) REVERT: C 107 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: C 111 ASN cc_start: 0.8323 (t0) cc_final: 0.8099 (t0) REVERT: C 182 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8881 (tp) REVERT: C 183 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7988 (mm-30) REVERT: C 189 ASP cc_start: 0.7717 (m-30) cc_final: 0.7385 (m-30) REVERT: C 363 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7736 (tp30) REVERT: C 386 ASN cc_start: 0.8105 (m-40) cc_final: 0.7891 (m110) REVERT: C 496 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7803 (pp20) REVERT: D 15 GLN cc_start: 0.8596 (mt0) cc_final: 0.8180 (tt0) REVERT: D 107 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: D 111 ASN cc_start: 0.8420 (t0) cc_final: 0.8185 (t0) REVERT: D 162 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: D 203 THR cc_start: 0.8681 (p) cc_final: 0.8428 (p) REVERT: D 306 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.8165 (mtp85) REVERT: D 363 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7666 (tp30) REVERT: D 386 ASN cc_start: 0.8093 (m-40) cc_final: 0.7799 (m110) REVERT: D 496 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: E 26 THR cc_start: 0.8327 (p) cc_final: 0.8051 (p) REVERT: E 107 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: E 191 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: E 362 MET cc_start: 0.9002 (mtp) cc_final: 0.8630 (mtp) REVERT: F 3 GLU cc_start: 0.8273 (pt0) cc_final: 0.7620 (mm-30) REVERT: F 111 ASN cc_start: 0.8283 (t0) cc_final: 0.8065 (t0) REVERT: F 183 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7945 (mm-30) REVERT: F 363 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7735 (tp30) REVERT: F 496 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7792 (pp20) REVERT: G 3 GLU cc_start: 0.8084 (pt0) cc_final: 0.7799 (pt0) REVERT: G 171 ASP cc_start: 0.7422 (t0) cc_final: 0.6971 (t0) REVERT: G 480 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8657 (mt-10) REVERT: G 485 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7593 (mt-10) REVERT: H 169 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8940 (p) REVERT: H 298 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8166 (mm-30) REVERT: H 306 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.8072 (mmt180) REVERT: H 480 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8529 (mt-10) REVERT: H 538 MET cc_start: 0.9104 (mtm) cc_final: 0.8828 (mtp) REVERT: I 13 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8071 (mt-10) REVERT: I 91 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6058 (m-30) REVERT: I 183 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: I 363 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7499 (tp30) REVERT: J 171 ASP cc_start: 0.7457 (t0) cc_final: 0.7124 (t0) REVERT: J 192 TYR cc_start: 0.8688 (t80) cc_final: 0.8296 (t80) REVERT: J 480 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8648 (mt-10) REVERT: J 485 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7623 (mt-10) REVERT: K 107 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: K 298 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8136 (mm-30) REVERT: K 306 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7961 (mmt180) REVERT: K 480 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8565 (mt-10) REVERT: L 13 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8035 (mt-10) REVERT: L 183 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: L 330 ASP cc_start: 0.8050 (p0) cc_final: 0.7846 (p0) REVERT: L 363 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7507 (tp30) REVERT: M 343 MET cc_start: 0.9119 (mmm) cc_final: 0.8869 (mmp) REVERT: N 107 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: N 194 ASP cc_start: 0.7594 (t0) cc_final: 0.7190 (m-30) REVERT: N 343 MET cc_start: 0.9221 (mmm) cc_final: 0.8977 (mmp) REVERT: N 480 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8662 (mt-10) REVERT: O 22 GLU cc_start: 0.8089 (tt0) cc_final: 0.7885 (tt0) REVERT: O 26 THR cc_start: 0.8665 (p) cc_final: 0.8454 (t) REVERT: O 435 ASP cc_start: 0.8373 (m-30) cc_final: 0.8126 (m-30) REVERT: P 107 GLU cc_start: 0.8212 (tp30) cc_final: 0.8005 (tp30) REVERT: P 343 MET cc_start: 0.9120 (mmm) cc_final: 0.8870 (mmp) REVERT: P 449 GLN cc_start: 0.8035 (pp30) cc_final: 0.7809 (pp30) REVERT: Q 194 ASP cc_start: 0.7572 (t0) cc_final: 0.7177 (m-30) REVERT: Q 480 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8658 (mt-10) REVERT: R 22 GLU cc_start: 0.8066 (tt0) cc_final: 0.7834 (tt0) REVERT: R 183 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7702 (tp30) outliers start: 213 outliers final: 102 residues processed: 1017 average time/residue: 1.5350 time to fit residues: 2010.5821 Evaluate side-chains 948 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 827 time to evaluate : 5.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 554 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 431 LYS Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 554 VAL Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 554 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 554 VAL Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 554 VAL Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 190 ILE Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 183 GLU Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 554 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 434 optimal weight: 9.9990 chunk 571 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 545 optimal weight: 10.0000 chunk 555 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 779 optimal weight: 6.9990 chunk 842 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 151 HIS B 47 ASN B 111 ASN C 47 ASN C 151 HIS D 47 ASN D 151 HIS E 47 ASN E 111 ASN E 131 ASN F 151 HIS G 355 ASN G 428 ASN ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN J 428 ASN K 15 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 ASN M 47 ASN P 47 ASN P 355 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.124471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.100355 restraints weight = 76681.113| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.17 r_work: 0.2795 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 69552 Z= 0.335 Angle : 0.674 17.668 94626 Z= 0.353 Chirality : 0.051 0.195 10098 Planarity : 0.005 0.071 12816 Dihedral : 5.341 141.570 9492 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.08 % Allowed : 12.28 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.74 (0.08), residues: 8694 helix: 0.40 (0.11), residues: 2304 sheet: 0.72 (0.12), residues: 1512 loop : -1.38 (0.08), residues: 4878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 489 HIS 0.007 0.002 HIS L 396 PHE 0.012 0.002 PHE A 478 TYR 0.017 0.003 TYR D 401 ARG 0.004 0.001 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 301 poor density : 853 time to evaluate : 5.885 Fit side-chains REVERT: A 15 GLN cc_start: 0.8623 (mt0) cc_final: 0.8231 (tt0) REVERT: A 107 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: A 111 ASN cc_start: 0.8451 (t0) cc_final: 0.8185 (t0) REVERT: A 192 TYR cc_start: 0.8784 (t80) cc_final: 0.8583 (t80) REVERT: A 306 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8152 (mtp85) REVERT: A 363 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7756 (tp30) REVERT: A 386 ASN cc_start: 0.8097 (m-40) cc_final: 0.7805 (m110) REVERT: A 496 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (pp20) REVERT: B 47 ASN cc_start: 0.8227 (t0) cc_final: 0.8024 (p0) REVERT: B 107 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: B 162 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: B 191 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: B 295 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8505 (tttp) REVERT: B 551 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8362 (mm-30) REVERT: C 107 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: C 111 ASN cc_start: 0.8187 (t0) cc_final: 0.7940 (t0) REVERT: C 154 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7390 (ttm-80) REVERT: C 183 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8007 (mm-30) REVERT: C 363 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7714 (tp30) REVERT: C 496 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7871 (pp20) REVERT: D 15 GLN cc_start: 0.8617 (mt0) cc_final: 0.8203 (tt0) REVERT: D 107 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: D 111 ASN cc_start: 0.8429 (t0) cc_final: 0.8181 (t0) REVERT: D 162 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: D 183 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7988 (mm-30) REVERT: D 306 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8171 (mtp85) REVERT: D 363 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7749 (tp30) REVERT: D 381 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9186 (mm) REVERT: D 386 ASN cc_start: 0.8132 (m-40) cc_final: 0.7843 (m110) REVERT: D 496 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: E 47 ASN cc_start: 0.8185 (t0) cc_final: 0.7946 (p0) REVERT: E 107 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: E 162 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: E 182 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8994 (tp) REVERT: E 191 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: E 427 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7862 (m90) REVERT: E 551 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8360 (mm-30) REVERT: F 3 GLU cc_start: 0.8196 (pt0) cc_final: 0.7598 (mm-30) REVERT: F 52 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: F 111 ASN cc_start: 0.8208 (t0) cc_final: 0.7912 (t0) REVERT: F 183 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8061 (mm-30) REVERT: F 363 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7729 (tp30) REVERT: F 496 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7898 (pp20) REVERT: G 3 GLU cc_start: 0.8172 (pt0) cc_final: 0.7880 (pt0) REVERT: G 115 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: G 171 ASP cc_start: 0.7379 (t0) cc_final: 0.6991 (t0) REVERT: G 485 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7650 (mt-10) REVERT: H 169 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8926 (p) REVERT: H 298 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8165 (mm-30) REVERT: H 306 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.8055 (mmt180) REVERT: H 480 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8575 (mt-10) REVERT: I 13 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8118 (mt-10) REVERT: I 91 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6223 (m-30) REVERT: I 183 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: I 330 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7911 (p0) REVERT: I 363 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7528 (tp30) REVERT: I 431 LYS cc_start: 0.8673 (tttm) cc_final: 0.8472 (ttmm) REVERT: J 52 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8030 (tt0) REVERT: J 171 ASP cc_start: 0.7462 (t0) cc_final: 0.7093 (t0) REVERT: J 192 TYR cc_start: 0.8726 (t80) cc_final: 0.8389 (t80) REVERT: J 485 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7715 (mt-10) REVERT: J 496 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8123 (pp20) REVERT: K 107 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: K 199 VAL cc_start: 0.8241 (m) cc_final: 0.8041 (p) REVERT: K 298 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8164 (mm-30) REVERT: K 480 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8595 (mt-10) REVERT: L 13 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8125 (mt-10) REVERT: L 183 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: L 330 ASP cc_start: 0.8015 (p0) cc_final: 0.7810 (p0) REVERT: L 363 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7516 (tp30) REVERT: N 107 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: N 194 ASP cc_start: 0.7630 (t0) cc_final: 0.7237 (m-30) REVERT: N 343 MET cc_start: 0.9243 (mmm) cc_final: 0.8996 (mmp) REVERT: N 496 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8100 (pp20) REVERT: O 22 GLU cc_start: 0.8167 (tt0) cc_final: 0.7888 (tt0) REVERT: O 435 ASP cc_start: 0.8346 (m-30) cc_final: 0.8092 (m-30) REVERT: O 496 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8040 (pp20) REVERT: O 540 GLU cc_start: 0.8240 (mp0) cc_final: 0.7917 (pt0) REVERT: P 449 GLN cc_start: 0.7965 (pp30) cc_final: 0.7742 (pp30) REVERT: P 496 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8227 (pp20) REVERT: Q 194 ASP cc_start: 0.7626 (t0) cc_final: 0.7237 (m-30) REVERT: Q 496 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8114 (pp20) REVERT: R 22 GLU cc_start: 0.8146 (tt0) cc_final: 0.7876 (tt0) REVERT: R 149 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7327 (mtpt) REVERT: R 194 ASP cc_start: 0.7485 (t0) cc_final: 0.6927 (m-30) REVERT: R 496 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8075 (pp20) outliers start: 301 outliers final: 152 residues processed: 1058 average time/residue: 1.4962 time to fit residues: 2055.0401 Evaluate side-chains 993 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 806 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 554 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 431 LYS Chi-restraints excluded: chain G residue 544 ASP Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 428 ASN Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 330 ASP Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 554 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 431 LYS Chi-restraints excluded: chain J residue 496 GLU Chi-restraints excluded: chain J residue 544 ASP Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 428 ASN Chi-restraints excluded: chain K residue 431 LYS Chi-restraints excluded: chain K residue 554 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 554 VAL Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 359 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 554 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 496 GLU Chi-restraints excluded: chain N residue 554 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 195 ASP Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 385 THR Chi-restraints excluded: chain O residue 496 GLU Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 359 VAL Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 386 ASN Chi-restraints excluded: chain P residue 496 GLU Chi-restraints excluded: chain P residue 554 VAL Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 190 ILE Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 359 VAL Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 496 GLU Chi-restraints excluded: chain Q residue 554 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain R residue 195 ASP Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 496 GLU Chi-restraints excluded: chain R residue 554 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 31 optimal weight: 3.9990 chunk 286 optimal weight: 0.0270 chunk 400 optimal weight: 20.0000 chunk 823 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 820 optimal weight: 0.0970 chunk 643 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 829 optimal weight: 20.0000 chunk 270 optimal weight: 6.9990 overall best weight: 3.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 151 HIS A 427 HIS B 111 ASN C 47 ASN C 151 HIS D 47 ASN D 151 HIS E 111 ASN E 131 ASN F 151 HIS G 427 HIS H 47 ASN H 355 ASN H 427 HIS I 47 ASN I 428 ASN J 355 ASN J 427 HIS K 47 ASN K 427 HIS L 47 ASN L 428 ASN M 47 ASN O 15 GLN P 47 ASN R 15 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.126961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.102775 restraints weight = 76605.389| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.19 r_work: 0.2824 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 69552 Z= 0.208 Angle : 0.567 13.486 94626 Z= 0.296 Chirality : 0.048 0.143 10098 Planarity : 0.004 0.058 12816 Dihedral : 4.967 142.538 9492 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.17 % Allowed : 13.10 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.44 (0.08), residues: 8694 helix: 0.83 (0.11), residues: 2304 sheet: 0.59 (0.11), residues: 1764 loop : -1.27 (0.08), residues: 4626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 140 HIS 0.005 0.001 HIS E 339 PHE 0.010 0.001 PHE Q 347 TYR 0.015 0.002 TYR D 401 ARG 0.006 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 308 poor density : 832 time to evaluate : 5.848 Fit side-chains REVERT: A 15 GLN cc_start: 0.8606 (mt0) cc_final: 0.8164 (tt0) REVERT: A 107 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: A 111 ASN cc_start: 0.8457 (t0) cc_final: 0.8220 (t0) REVERT: A 183 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8054 (mm-30) REVERT: A 195 ASP cc_start: 0.7749 (m-30) cc_final: 0.7515 (m-30) REVERT: A 306 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8182 (mtp85) REVERT: A 350 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8730 (mt) REVERT: A 363 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7725 (tp30) REVERT: A 386 ASN cc_start: 0.8103 (m-40) cc_final: 0.7794 (m110) REVERT: A 496 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: B 191 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: B 295 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8510 (tttp) REVERT: B 551 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8491 (mm-30) REVERT: C 107 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: C 111 ASN cc_start: 0.8218 (t0) cc_final: 0.7930 (t0) REVERT: C 154 ARG cc_start: 0.7764 (mmt90) cc_final: 0.7232 (ttm-80) REVERT: C 183 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8064 (mm-30) REVERT: C 363 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7885 (tp30) REVERT: C 496 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7707 (pp20) REVERT: D 15 GLN cc_start: 0.8602 (mt0) cc_final: 0.8173 (tt0) REVERT: D 107 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: D 111 ASN cc_start: 0.8458 (t0) cc_final: 0.8226 (t0) REVERT: D 306 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8173 (mtp85) REVERT: D 350 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8728 (mt) REVERT: D 363 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7742 (tp30) REVERT: D 386 ASN cc_start: 0.8126 (m-40) cc_final: 0.7832 (m110) REVERT: D 496 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7901 (pp20) REVERT: E 182 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8973 (tp) REVERT: E 191 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: E 551 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8475 (mm-30) REVERT: F 3 GLU cc_start: 0.8209 (pt0) cc_final: 0.7588 (mm-30) REVERT: F 52 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: F 111 ASN cc_start: 0.8185 (t0) cc_final: 0.7889 (t0) REVERT: F 183 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8037 (mm-30) REVERT: F 363 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7888 (tp30) REVERT: F 496 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7728 (pp20) REVERT: G 171 ASP cc_start: 0.7559 (t0) cc_final: 0.7098 (t0) REVERT: G 431 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8305 (tttm) REVERT: H 162 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: H 306 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.8020 (mmt180) REVERT: I 13 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8170 (mt-10) REVERT: I 91 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6346 (m-30) REVERT: I 183 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: I 330 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8038 (p0) REVERT: I 363 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7538 (tp30) REVERT: I 496 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7612 (pp20) REVERT: J 115 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: J 171 ASP cc_start: 0.7387 (t0) cc_final: 0.7018 (t0) REVERT: J 192 TYR cc_start: 0.8706 (t80) cc_final: 0.8366 (t80) REVERT: J 431 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8338 (tttm) REVERT: K 107 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: L 13 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8181 (mt-10) REVERT: L 183 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: L 330 ASP cc_start: 0.8149 (p0) cc_final: 0.7921 (p0) REVERT: L 363 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7557 (tp30) REVERT: L 431 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8173 (tttm) REVERT: M 15 GLN cc_start: 0.8594 (mt0) cc_final: 0.8376 (mt0) REVERT: M 91 ASP cc_start: 0.7127 (t0) cc_final: 0.6714 (p0) REVERT: M 343 MET cc_start: 0.9091 (mmm) cc_final: 0.8806 (mmp) REVERT: N 194 ASP cc_start: 0.7637 (t0) cc_final: 0.7249 (m-30) REVERT: N 343 MET cc_start: 0.9244 (mmm) cc_final: 0.9003 (mmp) REVERT: N 350 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8800 (mt) REVERT: O 22 GLU cc_start: 0.8266 (tt0) cc_final: 0.7955 (tt0) REVERT: O 496 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7980 (pp20) REVERT: O 540 GLU cc_start: 0.8239 (mp0) cc_final: 0.7888 (pt0) REVERT: P 91 ASP cc_start: 0.7202 (t0) cc_final: 0.6828 (p0) REVERT: P 343 MET cc_start: 0.9087 (mmm) cc_final: 0.8821 (mmp) REVERT: Q 194 ASP cc_start: 0.7622 (t0) cc_final: 0.7237 (m-30) REVERT: Q 350 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8791 (mt) REVERT: R 22 GLU cc_start: 0.8223 (tt0) cc_final: 0.7952 (tt0) REVERT: R 496 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: R 540 GLU cc_start: 0.8212 (mp0) cc_final: 0.7889 (pt0) outliers start: 308 outliers final: 160 residues processed: 1056 average time/residue: 1.4546 time to fit residues: 2004.4175 Evaluate side-chains 975 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 786 time to evaluate : 5.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 496 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 554 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 431 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 162 GLU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 330 ASP Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 496 GLU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 115 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 431 LYS Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 428 ASN Chi-restraints excluded: chain K residue 431 LYS Chi-restraints excluded: chain K residue 554 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 431 LYS Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 359 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 427 HIS Chi-restraints excluded: chain M residue 554 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 428 ASN Chi-restraints excluded: chain N residue 433 GLU Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 496 GLU Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 359 VAL Chi-restraints excluded: chain P residue 381 LEU Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 554 VAL Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 350 LEU Chi-restraints excluded: chain Q residue 359 VAL Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 428 ASN Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 554 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 496 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 110 optimal weight: 30.0000 chunk 260 optimal weight: 20.0000 chunk 777 optimal weight: 9.9990 chunk 713 optimal weight: 8.9990 chunk 423 optimal weight: 4.9990 chunk 420 optimal weight: 9.9990 chunk 808 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 814 optimal weight: 10.0000 chunk 759 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 151 HIS C 47 ASN C 151 HIS D 47 ASN D 151 HIS E 47 ASN E 131 ASN F 151 HIS K 47 ASN K 355 ASN M 47 ASN P 15 GLN P 47 ASN R 15 GLN R 111 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.123107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.099099 restraints weight = 76872.004| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.15 r_work: 0.2780 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 69552 Z= 0.414 Angle : 0.727 18.667 94626 Z= 0.382 Chirality : 0.053 0.234 10098 Planarity : 0.006 0.078 12816 Dihedral : 5.460 140.381 9492 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.97 % Allowed : 13.10 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.08), residues: 8694 helix: 0.59 (0.11), residues: 2304 sheet: 0.83 (0.12), residues: 1512 loop : -1.21 (0.08), residues: 4878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 489 HIS 0.013 0.002 HIS A 151 PHE 0.014 0.002 PHE A 478 TYR 0.018 0.003 TYR A 401 ARG 0.005 0.001 ARG H 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 367 poor density : 811 time to evaluate : 5.891 Fit side-chains REVERT: A 15 GLN cc_start: 0.8651 (mt0) cc_final: 0.8247 (tt0) REVERT: A 107 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: A 111 ASN cc_start: 0.8422 (t0) cc_final: 0.8185 (t0) REVERT: A 183 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8085 (mm-30) REVERT: A 195 ASP cc_start: 0.7660 (m-30) cc_final: 0.7426 (m-30) REVERT: A 306 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8146 (mtp85) REVERT: A 350 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8758 (mt) REVERT: A 363 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7725 (tp30) REVERT: A 386 ASN cc_start: 0.8119 (m-40) cc_final: 0.7840 (m110) REVERT: A 496 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8189 (pp20) REVERT: B 12 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: B 60 LYS cc_start: 0.8493 (pttp) cc_final: 0.8039 (ptmm) REVERT: B 107 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: B 191 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8106 (tm-30) REVERT: B 535 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 551 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8438 (mm-30) REVERT: C 107 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: C 111 ASN cc_start: 0.8228 (t0) cc_final: 0.7972 (t0) REVERT: C 154 ARG cc_start: 0.7822 (mmt90) cc_final: 0.7191 (ttm-80) REVERT: C 183 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8109 (mm-30) REVERT: C 363 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7834 (tp30) REVERT: C 496 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: D 15 GLN cc_start: 0.8616 (mt0) cc_final: 0.8229 (tt0) REVERT: D 107 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: D 111 ASN cc_start: 0.8439 (t0) cc_final: 0.8229 (t0) REVERT: D 183 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: D 306 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.8133 (mtp85) REVERT: D 350 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8759 (mt) REVERT: D 363 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7703 (tp30) REVERT: D 381 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9199 (mm) REVERT: D 386 ASN cc_start: 0.8123 (m-40) cc_final: 0.7865 (m110) REVERT: E 12 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: E 107 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: E 182 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8995 (tp) REVERT: E 191 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: E 427 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7933 (m90) REVERT: E 535 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: E 551 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8424 (mm-30) REVERT: F 3 GLU cc_start: 0.8153 (pt0) cc_final: 0.7595 (mm-30) REVERT: F 52 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: F 111 ASN cc_start: 0.8234 (t0) cc_final: 0.7957 (t0) REVERT: F 183 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8068 (mm-30) REVERT: F 363 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7812 (tp30) REVERT: F 496 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7866 (pp20) REVERT: G 111 ASN cc_start: 0.8286 (t0) cc_final: 0.8028 (t0) REVERT: G 171 ASP cc_start: 0.7496 (t0) cc_final: 0.7017 (t0) REVERT: G 485 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7284 (mm-30) REVERT: H 162 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: H 306 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7903 (mtt180) REVERT: I 3 GLU cc_start: 0.8202 (pt0) cc_final: 0.7792 (mm-30) REVERT: I 13 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8165 (mt-10) REVERT: I 91 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: I 162 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: I 183 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: I 191 GLU cc_start: 0.8365 (tt0) cc_final: 0.7953 (tp30) REVERT: I 330 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8055 (p0) REVERT: I 350 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8956 (mt) REVERT: I 363 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7579 (tp30) REVERT: J 115 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: J 171 ASP cc_start: 0.7474 (t0) cc_final: 0.7192 (t0) REVERT: J 192 TYR cc_start: 0.8754 (t80) cc_final: 0.8450 (t80) REVERT: J 485 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: K 50 ASP cc_start: 0.8347 (m-30) cc_final: 0.8093 (m-30) REVERT: K 107 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: K 162 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: L 13 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8151 (mt-10) REVERT: L 162 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: L 183 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: L 350 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8948 (mt) REVERT: L 363 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7605 (tp30) REVERT: M 350 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8817 (mt) REVERT: N 173 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7221 (mp0) REVERT: N 183 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8162 (tp30) REVERT: N 194 ASP cc_start: 0.7691 (t0) cc_final: 0.7309 (m-30) REVERT: N 343 MET cc_start: 0.9215 (mmm) cc_final: 0.8985 (mmp) REVERT: N 350 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8840 (mt) REVERT: O 149 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.6911 (mmtm) REVERT: O 387 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7472 (mtt90) REVERT: O 496 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8004 (pp20) REVERT: O 540 GLU cc_start: 0.8196 (mp0) cc_final: 0.7915 (pt0) REVERT: P 15 GLN cc_start: 0.8724 (mt0) cc_final: 0.8413 (mt0) REVERT: P 350 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8808 (mt) REVERT: Q 194 ASP cc_start: 0.7677 (t0) cc_final: 0.7296 (m-30) REVERT: Q 350 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8836 (mt) REVERT: R 149 LYS cc_start: 0.7741 (mtpt) cc_final: 0.6943 (mmtm) REVERT: R 194 ASP cc_start: 0.7495 (t0) cc_final: 0.6953 (m-30) REVERT: R 387 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7487 (mtt90) REVERT: R 496 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8151 (pp20) REVERT: R 540 GLU cc_start: 0.8153 (mp0) cc_final: 0.7898 (pt0) outliers start: 367 outliers final: 221 residues processed: 1071 average time/residue: 1.4400 time to fit residues: 2012.8177 Evaluate side-chains 1039 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 773 time to evaluate : 5.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 427 HIS Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 535 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 554 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 431 LYS Chi-restraints excluded: chain G residue 485 GLU Chi-restraints excluded: chain G residue 544 ASP Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 162 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 428 ASN Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 330 ASP Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 554 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 115 GLN Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 431 LYS Chi-restraints excluded: chain J residue 485 GLU Chi-restraints excluded: chain J residue 544 ASP Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 428 ASN Chi-restraints excluded: chain K residue 431 LYS Chi-restraints excluded: chain K residue 554 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 381 LEU Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 554 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 359 VAL Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 ASN Chi-restraints excluded: chain M residue 427 HIS Chi-restraints excluded: chain M residue 554 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 428 ASN Chi-restraints excluded: chain N residue 433 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 554 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 149 LYS Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 496 GLU Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 350 LEU Chi-restraints excluded: chain P residue 359 VAL Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 386 ASN Chi-restraints excluded: chain P residue 427 HIS Chi-restraints excluded: chain P residue 554 VAL Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 190 ILE Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 350 LEU Chi-restraints excluded: chain Q residue 359 VAL Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 428 ASN Chi-restraints excluded: chain Q residue 433 GLU Chi-restraints excluded: chain Q residue 487 THR Chi-restraints excluded: chain Q residue 554 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 387 ARG Chi-restraints excluded: chain R residue 496 GLU Chi-restraints excluded: chain R residue 554 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 305 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 516 optimal weight: 8.9990 chunk 820 optimal weight: 0.0970 chunk 834 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 508 optimal weight: 2.9990 chunk 312 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 856 optimal weight: 0.8980 chunk 495 optimal weight: 0.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS C 151 HIS D 151 HIS E 47 ASN E 131 ASN F 151 HIS M 47 ASN P 47 ASN R 111 ASN R 181 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.128568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.104511 restraints weight = 76283.366| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.16 r_work: 0.2862 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 69552 Z= 0.156 Angle : 0.517 11.049 94626 Z= 0.271 Chirality : 0.046 0.134 10098 Planarity : 0.004 0.063 12816 Dihedral : 4.734 139.621 9492 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.62 % Allowed : 14.92 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.13 (0.09), residues: 8694 helix: 1.09 (0.11), residues: 2304 sheet: 0.77 (0.12), residues: 1746 loop : -1.05 (0.08), residues: 4644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 456 HIS 0.004 0.001 HIS E 339 PHE 0.009 0.001 PHE A 478 TYR 0.015 0.001 TYR A 401 ARG 0.006 0.000 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 789 time to evaluate : 5.851 Fit side-chains REVERT: A 3 GLU cc_start: 0.8287 (pt0) cc_final: 0.7478 (mm-30) REVERT: A 15 GLN cc_start: 0.8615 (mt0) cc_final: 0.8188 (tt0) REVERT: A 107 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: A 111 ASN cc_start: 0.8497 (t0) cc_final: 0.8163 (t0) REVERT: A 183 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8002 (mm-30) REVERT: A 192 TYR cc_start: 0.8684 (t80) cc_final: 0.8385 (t80) REVERT: A 195 ASP cc_start: 0.7721 (m-30) cc_final: 0.7393 (m-30) REVERT: A 306 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8180 (mtp85) REVERT: A 350 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8771 (mt) REVERT: A 363 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7666 (tp30) REVERT: A 386 ASN cc_start: 0.8207 (m-40) cc_final: 0.7926 (m110) REVERT: B 60 LYS cc_start: 0.8470 (pttp) cc_final: 0.7998 (ptmm) REVERT: B 107 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: B 191 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: B 551 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8595 (mm-30) REVERT: C 111 ASN cc_start: 0.8211 (t0) cc_final: 0.7915 (t0) REVERT: C 154 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7229 (ttm-80) REVERT: C 183 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8140 (mm-30) REVERT: C 363 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7831 (tp30) REVERT: C 496 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7678 (pp20) REVERT: D 3 GLU cc_start: 0.8292 (pt0) cc_final: 0.7495 (mm-30) REVERT: D 15 GLN cc_start: 0.8587 (mt0) cc_final: 0.8150 (tt0) REVERT: D 107 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: D 111 ASN cc_start: 0.8494 (t0) cc_final: 0.8177 (t0) REVERT: D 183 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: D 306 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8161 (mtp85) REVERT: D 350 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8776 (mt) REVERT: D 363 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7647 (tp30) REVERT: D 386 ASN cc_start: 0.8220 (m-40) cc_final: 0.7944 (m110) REVERT: E 149 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7347 (mmmt) REVERT: E 191 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: E 551 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8572 (mm-30) REVERT: F 3 GLU cc_start: 0.8179 (pt0) cc_final: 0.7520 (mm-30) REVERT: F 52 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: F 111 ASN cc_start: 0.8200 (t0) cc_final: 0.7896 (t0) REVERT: F 183 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8053 (mm-30) REVERT: F 363 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7791 (tp30) REVERT: F 496 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: G 171 ASP cc_start: 0.7630 (t0) cc_final: 0.7119 (t0) REVERT: G 192 TYR cc_start: 0.8469 (t80) cc_final: 0.8257 (t80) REVERT: G 195 ASP cc_start: 0.7367 (m-30) cc_final: 0.7070 (m-30) REVERT: G 431 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8246 (tttm) REVERT: H 497 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7774 (mm-40) REVERT: H 538 MET cc_start: 0.9032 (mtm) cc_final: 0.8645 (mtp) REVERT: I 13 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8256 (mt-10) REVERT: I 91 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6409 (m-30) REVERT: I 183 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: I 330 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8048 (p0) REVERT: I 350 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8970 (mt) REVERT: I 496 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7558 (pp20) REVERT: J 171 ASP cc_start: 0.7447 (t0) cc_final: 0.7077 (t0) REVERT: J 192 TYR cc_start: 0.8770 (t80) cc_final: 0.8376 (t80) REVERT: J 431 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8265 (tttm) REVERT: K 50 ASP cc_start: 0.8261 (m-30) cc_final: 0.7980 (m-30) REVERT: K 107 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: K 497 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7794 (mm-40) REVERT: K 538 MET cc_start: 0.9063 (mtm) cc_final: 0.8673 (mtp) REVERT: L 13 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8273 (mt-10) REVERT: L 183 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: L 350 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8961 (mt) REVERT: L 363 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7550 (tp30) REVERT: M 91 ASP cc_start: 0.7255 (t0) cc_final: 0.6760 (p0) REVERT: M 343 MET cc_start: 0.9079 (mmm) cc_final: 0.8840 (mmp) REVERT: M 350 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8917 (mt) REVERT: N 194 ASP cc_start: 0.7708 (t0) cc_final: 0.7329 (m-30) REVERT: N 343 MET cc_start: 0.9188 (mmm) cc_final: 0.8968 (mmp) REVERT: N 350 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8777 (mt) REVERT: O 149 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6905 (mmtm) REVERT: O 195 ASP cc_start: 0.7663 (m-30) cc_final: 0.7437 (t0) REVERT: O 496 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7805 (pp20) REVERT: O 540 GLU cc_start: 0.8234 (mp0) cc_final: 0.7934 (pt0) REVERT: P 91 ASP cc_start: 0.7236 (t0) cc_final: 0.6806 (p0) REVERT: P 343 MET cc_start: 0.9062 (mmm) cc_final: 0.8818 (mmp) REVERT: P 350 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8908 (mt) REVERT: Q 194 ASP cc_start: 0.7738 (t0) cc_final: 0.7361 (m-30) REVERT: Q 350 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8773 (mt) REVERT: R 149 LYS cc_start: 0.7747 (mtpt) cc_final: 0.6984 (mmtm) REVERT: R 496 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7978 (pp20) REVERT: R 540 GLU cc_start: 0.8215 (mp0) cc_final: 0.7910 (pt0) outliers start: 267 outliers final: 146 residues processed: 986 average time/residue: 1.4435 time to fit residues: 1855.6706 Evaluate side-chains 939 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 765 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 496 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 151 HIS Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 554 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 431 LYS Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 428 ASN Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 330 ASP Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 496 GLU Chi-restraints excluded: chain I residue 554 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 431 LYS Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 350 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 428 ASN Chi-restraints excluded: chain K residue 554 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 381 LEU Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 554 VAL Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 427 HIS Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 485 GLU Chi-restraints excluded: chain N residue 496 GLU Chi-restraints excluded: chain N residue 554 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 149 LYS Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 496 GLU Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 350 LEU Chi-restraints excluded: chain P residue 381 LEU Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 427 HIS Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 350 LEU Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 485 GLU Chi-restraints excluded: chain Q residue 496 GLU Chi-restraints excluded: chain Q residue 554 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 496 GLU Chi-restraints excluded: chain R residue 554 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 455 optimal weight: 10.0000 chunk 574 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 568 optimal weight: 8.9990 chunk 321 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 413 optimal weight: 0.7980 chunk 632 optimal weight: 0.9980 chunk 660 optimal weight: 9.9990 chunk 344 optimal weight: 30.0000 chunk 240 optimal weight: 8.9990 overall best weight: 4.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 428 ASN C 151 HIS D 151 HIS E 131 ASN F 151 HIS H 131 ASN K 131 ASN M 47 ASN N 47 ASN O 111 ASN P 47 ASN R 111 ASN R 181 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.126617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.101811 restraints weight = 76090.623| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.19 r_work: 0.2788 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 69552 Z= 0.230 Angle : 0.581 14.219 94626 Z= 0.304 Chirality : 0.048 0.147 10098 Planarity : 0.004 0.059 12816 Dihedral : 4.412 17.571 9486 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.81 % Allowed : 14.91 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.09), residues: 8694 helix: 1.11 (0.11), residues: 2304 sheet: 0.80 (0.12), residues: 1746 loop : -1.04 (0.08), residues: 4644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 140 HIS 0.005 0.001 HIS P 339 PHE 0.010 0.001 PHE A 478 TYR 0.014 0.002 TYR D 401 ARG 0.005 0.000 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 760 time to evaluate : 5.835 Fit side-chains REVERT: A 3 GLU cc_start: 0.8304 (pt0) cc_final: 0.7463 (mm-30) REVERT: A 15 GLN cc_start: 0.8613 (mt0) cc_final: 0.8179 (tt0) REVERT: A 107 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: A 111 ASN cc_start: 0.8554 (t0) cc_final: 0.8234 (t0) REVERT: A 183 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8082 (mm-30) REVERT: A 195 ASP cc_start: 0.7723 (m-30) cc_final: 0.7378 (m-30) REVERT: A 306 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8184 (mtp85) REVERT: A 350 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8709 (mt) REVERT: A 363 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7700 (tp30) REVERT: A 386 ASN cc_start: 0.8254 (m-40) cc_final: 0.7960 (m110) REVERT: B 107 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: B 191 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: B 551 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8617 (mm-30) REVERT: C 107 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: C 111 ASN cc_start: 0.8227 (t0) cc_final: 0.7928 (t0) REVERT: C 154 ARG cc_start: 0.7750 (mmt90) cc_final: 0.7323 (ttm-80) REVERT: C 183 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: C 363 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7815 (tp30) REVERT: C 496 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7776 (pp20) REVERT: D 3 GLU cc_start: 0.8313 (pt0) cc_final: 0.7466 (mm-30) REVERT: D 15 GLN cc_start: 0.8594 (mt0) cc_final: 0.8160 (tt0) REVERT: D 107 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: D 111 ASN cc_start: 0.8545 (t0) cc_final: 0.8193 (t0) REVERT: D 183 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: D 192 TYR cc_start: 0.8721 (t80) cc_final: 0.8386 (t80) REVERT: D 195 ASP cc_start: 0.7823 (m-30) cc_final: 0.7480 (m-30) REVERT: D 306 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8172 (mtp85) REVERT: D 350 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8713 (mt) REVERT: D 363 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7667 (tp30) REVERT: D 386 ASN cc_start: 0.8232 (m-40) cc_final: 0.7948 (m110) REVERT: D 496 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8162 (pp20) REVERT: E 107 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: E 182 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8886 (tp) REVERT: E 191 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: E 551 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8595 (mm-30) REVERT: F 3 GLU cc_start: 0.8278 (pt0) cc_final: 0.7547 (mm-30) REVERT: F 52 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: F 111 ASN cc_start: 0.8229 (t0) cc_final: 0.7925 (t0) REVERT: F 183 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8121 (mm-30) REVERT: F 363 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7827 (tp30) REVERT: F 496 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7775 (pp20) REVERT: G 26 THR cc_start: 0.8739 (p) cc_final: 0.8455 (t) REVERT: G 171 ASP cc_start: 0.7656 (t0) cc_final: 0.7119 (t0) REVERT: G 195 ASP cc_start: 0.7385 (m-30) cc_final: 0.7096 (m-30) REVERT: G 431 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8303 (tttm) REVERT: H 162 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: H 183 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: H 431 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8495 (ttmm) REVERT: I 13 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8283 (mt-10) REVERT: I 91 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: I 183 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: I 191 GLU cc_start: 0.8286 (tt0) cc_final: 0.7878 (tp30) REVERT: I 350 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8972 (mt) REVERT: I 496 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: J 171 ASP cc_start: 0.7524 (t0) cc_final: 0.7150 (t0) REVERT: J 192 TYR cc_start: 0.8765 (t80) cc_final: 0.8466 (t80) REVERT: J 431 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8325 (tttm) REVERT: J 567 ILE cc_start: 0.9289 (mt) cc_final: 0.9063 (mm) REVERT: K 107 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: K 183 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8104 (mm-30) REVERT: L 13 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8296 (mt-10) REVERT: L 91 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6507 (m-30) REVERT: L 183 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: L 350 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8996 (mt) REVERT: L 363 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7593 (tp30) REVERT: M 91 ASP cc_start: 0.7251 (t0) cc_final: 0.6885 (p0) REVERT: M 350 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8842 (mt) REVERT: N 162 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8170 (mm-30) REVERT: N 194 ASP cc_start: 0.7728 (t0) cc_final: 0.7354 (m-30) REVERT: N 343 MET cc_start: 0.9235 (mmm) cc_final: 0.8989 (mmp) REVERT: N 350 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8802 (mt) REVERT: O 149 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.6881 (mmtm) REVERT: O 195 ASP cc_start: 0.7646 (m-30) cc_final: 0.7420 (t0) REVERT: O 496 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7943 (pp20) REVERT: O 540 GLU cc_start: 0.8219 (mp0) cc_final: 0.7919 (pt0) REVERT: P 91 ASP cc_start: 0.7192 (t0) cc_final: 0.6847 (p0) REVERT: P 350 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8835 (mt) REVERT: Q 162 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8172 (mm-30) REVERT: Q 194 ASP cc_start: 0.7715 (t0) cc_final: 0.7341 (m-30) REVERT: Q 350 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8795 (mt) REVERT: R 149 LYS cc_start: 0.7716 (mtpt) cc_final: 0.6914 (mmtm) REVERT: R 195 ASP cc_start: 0.7642 (m-30) cc_final: 0.7367 (t0) REVERT: R 496 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8083 (pp20) REVERT: R 540 GLU cc_start: 0.8221 (mp0) cc_final: 0.7896 (pt0) outliers start: 281 outliers final: 187 residues processed: 972 average time/residue: 1.4928 time to fit residues: 1881.3548 Evaluate side-chains 971 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 745 time to evaluate : 5.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 427 HIS Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 496 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 554 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 431 LYS Chi-restraints excluded: chain G residue 544 ASP Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 162 GLU Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 428 ASN Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 496 GLU Chi-restraints excluded: chain I residue 554 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 431 LYS Chi-restraints excluded: chain J residue 544 ASP Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 428 ASN Chi-restraints excluded: chain K residue 554 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 330 ASP Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 381 LEU Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 554 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 359 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 427 HIS Chi-restraints excluded: chain M residue 554 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 418 THR Chi-restraints excluded: chain N residue 428 ASN Chi-restraints excluded: chain N residue 433 GLU Chi-restraints excluded: chain N residue 485 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 496 GLU Chi-restraints excluded: chain N residue 554 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 149 LYS Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain O residue 496 GLU Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 350 LEU Chi-restraints excluded: chain P residue 359 VAL Chi-restraints excluded: chain P residue 381 LEU Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 427 HIS Chi-restraints excluded: chain P residue 554 VAL Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 162 GLU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 350 LEU Chi-restraints excluded: chain Q residue 359 VAL Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 418 THR Chi-restraints excluded: chain Q residue 428 ASN Chi-restraints excluded: chain Q residue 485 GLU Chi-restraints excluded: chain Q residue 487 THR Chi-restraints excluded: chain Q residue 496 GLU Chi-restraints excluded: chain Q residue 554 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 410 VAL Chi-restraints excluded: chain R residue 496 GLU Chi-restraints excluded: chain R residue 554 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 483 optimal weight: 6.9990 chunk 851 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 484 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 321 optimal weight: 9.9990 chunk 638 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 780 optimal weight: 30.0000 chunk 787 optimal weight: 9.9990 chunk 840 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 428 ASN C 151 HIS D 151 HIS E 131 ASN F 151 HIS M 47 ASN O 111 ASN P 47 ASN R 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.125679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.101328 restraints weight = 76119.606| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.16 r_work: 0.2784 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 69552 Z= 0.262 Angle : 0.610 15.164 94626 Z= 0.319 Chirality : 0.049 0.159 10098 Planarity : 0.005 0.057 12816 Dihedral : 4.542 17.850 9486 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.11 % Allowed : 14.78 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.12 (0.09), residues: 8694 helix: 1.02 (0.11), residues: 2304 sheet: 0.85 (0.12), residues: 1728 loop : -1.04 (0.08), residues: 4662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 489 HIS 0.005 0.002 HIS L 339 PHE 0.011 0.002 PHE A 478 TYR 0.015 0.002 TYR M 375 ARG 0.006 0.000 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 303 poor density : 767 time to evaluate : 5.862 Fit side-chains REVERT: A 15 GLN cc_start: 0.8647 (mt0) cc_final: 0.8229 (tt0) REVERT: A 111 ASN cc_start: 0.8525 (t0) cc_final: 0.8196 (t0) REVERT: A 183 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: A 306 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8177 (mtp85) REVERT: A 350 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8721 (mt) REVERT: A 363 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7665 (tp30) REVERT: A 386 ASN cc_start: 0.8236 (m-40) cc_final: 0.7947 (m110) REVERT: B 107 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: B 191 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: B 551 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8596 (mm-30) REVERT: C 107 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: C 111 ASN cc_start: 0.8264 (t0) cc_final: 0.7964 (t0) REVERT: C 154 ARG cc_start: 0.7790 (mmt90) cc_final: 0.7301 (ttm-80) REVERT: C 183 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: C 363 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7836 (tp30) REVERT: C 496 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7868 (pp20) REVERT: D 15 GLN cc_start: 0.8616 (mt0) cc_final: 0.8206 (tt0) REVERT: D 111 ASN cc_start: 0.8531 (t0) cc_final: 0.8193 (t0) REVERT: D 183 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: D 195 ASP cc_start: 0.7801 (m-30) cc_final: 0.7470 (m-30) REVERT: D 306 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8172 (mtp85) REVERT: D 350 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8717 (mt) REVERT: D 363 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7633 (tp30) REVERT: D 386 ASN cc_start: 0.8282 (m-40) cc_final: 0.7929 (m110) REVERT: D 496 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8145 (pp20) REVERT: E 107 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: E 182 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8907 (tp) REVERT: E 191 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: E 551 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8585 (mm-30) REVERT: F 3 GLU cc_start: 0.8278 (pt0) cc_final: 0.7549 (mm-30) REVERT: F 52 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: F 111 ASN cc_start: 0.8271 (t0) cc_final: 0.7966 (t0) REVERT: F 183 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8115 (mm-30) REVERT: F 363 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7837 (tp30) REVERT: F 496 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7860 (pp20) REVERT: G 171 ASP cc_start: 0.7686 (t0) cc_final: 0.7143 (t0) REVERT: G 195 ASP cc_start: 0.7426 (m-30) cc_final: 0.7122 (m-30) REVERT: G 431 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8258 (tttm) REVERT: H 162 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7531 (tp30) REVERT: H 183 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8152 (mm-30) REVERT: I 13 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8272 (mt-10) REVERT: I 91 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6534 (m-30) REVERT: I 162 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: I 183 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8119 (mm-30) REVERT: I 191 GLU cc_start: 0.8297 (tt0) cc_final: 0.7943 (tp30) REVERT: I 350 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8939 (mt) REVERT: I 496 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7593 (pp20) REVERT: J 171 ASP cc_start: 0.7512 (t0) cc_final: 0.7115 (t0) REVERT: J 192 TYR cc_start: 0.8745 (t80) cc_final: 0.8446 (t80) REVERT: J 431 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8288 (tttm) REVERT: J 567 ILE cc_start: 0.9292 (mt) cc_final: 0.9058 (mm) REVERT: K 107 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: K 162 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: K 183 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: L 13 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8280 (mt-10) REVERT: L 91 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6519 (m-30) REVERT: L 162 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: L 183 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: L 350 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8932 (mt) REVERT: L 363 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7623 (tp30) REVERT: M 91 ASP cc_start: 0.7161 (t0) cc_final: 0.6829 (p0) REVERT: M 350 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8853 (mt) REVERT: N 143 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5626 (m-30) REVERT: N 162 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8174 (mm-30) REVERT: N 194 ASP cc_start: 0.7739 (t0) cc_final: 0.7366 (m-30) REVERT: N 350 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8822 (mt) REVERT: O 149 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6863 (mmtm) REVERT: O 195 ASP cc_start: 0.7611 (m-30) cc_final: 0.7393 (t0) REVERT: O 496 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7964 (pp20) REVERT: O 540 GLU cc_start: 0.8236 (mp0) cc_final: 0.7935 (pt0) REVERT: P 91 ASP cc_start: 0.7107 (t0) cc_final: 0.6792 (p0) REVERT: P 350 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8848 (mt) REVERT: Q 143 ASP cc_start: 0.5899 (OUTLIER) cc_final: 0.5530 (m-30) REVERT: Q 162 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8180 (mm-30) REVERT: Q 194 ASP cc_start: 0.7723 (t0) cc_final: 0.7341 (m-30) REVERT: Q 350 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8813 (mt) REVERT: R 149 LYS cc_start: 0.7742 (mtpt) cc_final: 0.6902 (mmtm) REVERT: R 195 ASP cc_start: 0.7617 (m-30) cc_final: 0.7347 (t0) REVERT: R 496 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8058 (pp20) REVERT: R 540 GLU cc_start: 0.8266 (mp0) cc_final: 0.7893 (pt0) outliers start: 303 outliers final: 218 residues processed: 991 average time/residue: 1.4493 time to fit residues: 1871.6777 Evaluate side-chains 1008 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 748 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 427 HIS Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 496 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 554 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 431 LYS Chi-restraints excluded: chain G residue 544 ASP Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 162 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 428 ASN Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 496 GLU Chi-restraints excluded: chain I residue 554 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 431 LYS Chi-restraints excluded: chain J residue 544 ASP Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 350 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 428 ASN Chi-restraints excluded: chain K residue 431 LYS Chi-restraints excluded: chain K residue 554 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 330 ASP Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 381 LEU Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 554 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 359 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 427 HIS Chi-restraints excluded: chain M residue 554 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 143 ASP Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 418 THR Chi-restraints excluded: chain N residue 428 ASN Chi-restraints excluded: chain N residue 433 GLU Chi-restraints excluded: chain N residue 485 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 554 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 149 LYS Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain O residue 496 GLU Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 350 LEU Chi-restraints excluded: chain P residue 359 VAL Chi-restraints excluded: chain P residue 381 LEU Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 427 HIS Chi-restraints excluded: chain P residue 554 VAL Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain Q residue 162 GLU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 190 ILE Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 350 LEU Chi-restraints excluded: chain Q residue 359 VAL Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 418 THR Chi-restraints excluded: chain Q residue 428 ASN Chi-restraints excluded: chain Q residue 485 GLU Chi-restraints excluded: chain Q residue 487 THR Chi-restraints excluded: chain Q residue 554 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 410 VAL Chi-restraints excluded: chain R residue 496 GLU Chi-restraints excluded: chain R residue 554 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 78 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 406 optimal weight: 9.9990 chunk 689 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 222 optimal weight: 7.9990 chunk 656 optimal weight: 9.9990 chunk 501 optimal weight: 5.9990 chunk 758 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 428 ASN C 151 HIS D 151 HIS E 131 ASN F 151 HIS M 47 ASN O 111 ASN P 47 ASN R 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.101161 restraints weight = 76388.627| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.13 r_work: 0.2797 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 69552 Z= 0.280 Angle : 0.621 15.464 94626 Z= 0.325 Chirality : 0.049 0.168 10098 Planarity : 0.005 0.056 12816 Dihedral : 4.576 18.127 9486 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.11 % Allowed : 15.04 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.13 (0.09), residues: 8694 helix: 0.99 (0.11), residues: 2304 sheet: 0.90 (0.12), residues: 1566 loop : -0.98 (0.08), residues: 4824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 489 HIS 0.013 0.002 HIS D 151 PHE 0.011 0.002 PHE A 478 TYR 0.016 0.002 TYR M 375 ARG 0.006 0.000 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 303 poor density : 753 time to evaluate : 5.821 Fit side-chains REVERT: A 15 GLN cc_start: 0.8643 (mt0) cc_final: 0.8232 (tt0) REVERT: A 111 ASN cc_start: 0.8522 (t0) cc_final: 0.8183 (t0) REVERT: A 183 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8101 (mm-30) REVERT: A 306 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8168 (mtp85) REVERT: A 350 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8723 (mt) REVERT: A 363 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7659 (tp30) REVERT: A 386 ASN cc_start: 0.8321 (m-40) cc_final: 0.7954 (m110) REVERT: B 107 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: B 191 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: B 551 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8588 (mm-30) REVERT: C 107 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: C 111 ASN cc_start: 0.8266 (t0) cc_final: 0.7969 (t0) REVERT: C 154 ARG cc_start: 0.7785 (mmt90) cc_final: 0.7331 (ttm-80) REVERT: C 183 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: C 363 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7860 (tp30) REVERT: C 496 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7848 (pp20) REVERT: D 15 GLN cc_start: 0.8603 (mt0) cc_final: 0.8195 (tt0) REVERT: D 111 ASN cc_start: 0.8521 (t0) cc_final: 0.8175 (t0) REVERT: D 183 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8046 (mm-30) REVERT: D 195 ASP cc_start: 0.7795 (m-30) cc_final: 0.7468 (m-30) REVERT: D 306 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8164 (mtp85) REVERT: D 350 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8721 (mt) REVERT: D 363 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7623 (tp30) REVERT: D 386 ASN cc_start: 0.8288 (m-40) cc_final: 0.7936 (m110) REVERT: D 496 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8101 (pp20) REVERT: E 107 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: E 182 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8921 (tp) REVERT: E 191 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: E 551 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8576 (mm-30) REVERT: F 3 GLU cc_start: 0.8263 (pt0) cc_final: 0.7557 (mm-30) REVERT: F 52 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: F 111 ASN cc_start: 0.8271 (t0) cc_final: 0.7975 (t0) REVERT: F 183 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: F 363 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7862 (tp30) REVERT: F 496 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7847 (pp20) REVERT: G 171 ASP cc_start: 0.7679 (t0) cc_final: 0.7146 (t0) REVERT: G 195 ASP cc_start: 0.7417 (m-30) cc_final: 0.7119 (m-30) REVERT: G 431 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8308 (tttm) REVERT: G 567 ILE cc_start: 0.9283 (mt) cc_final: 0.9043 (mm) REVERT: H 162 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: H 183 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: I 3 GLU cc_start: 0.8220 (pt0) cc_final: 0.7758 (mm-30) REVERT: I 13 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8261 (mt-10) REVERT: I 91 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6555 (m-30) REVERT: I 162 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: I 183 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: I 191 GLU cc_start: 0.8286 (tt0) cc_final: 0.7936 (tp30) REVERT: I 350 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8935 (mt) REVERT: J 171 ASP cc_start: 0.7520 (t0) cc_final: 0.7134 (t0) REVERT: J 192 TYR cc_start: 0.8739 (t80) cc_final: 0.8501 (t80) REVERT: J 431 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8337 (tttm) REVERT: J 567 ILE cc_start: 0.9292 (mt) cc_final: 0.9057 (mm) REVERT: K 107 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: K 162 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: K 183 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8133 (mm-30) REVERT: L 3 GLU cc_start: 0.8255 (pt0) cc_final: 0.7776 (mm-30) REVERT: L 13 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8263 (mt-10) REVERT: L 91 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6526 (m-30) REVERT: L 162 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: L 183 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: L 350 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8930 (mt) REVERT: L 363 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7619 (tp30) REVERT: M 91 ASP cc_start: 0.7163 (t0) cc_final: 0.6849 (p0) REVERT: M 350 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8817 (mt) REVERT: N 143 ASP cc_start: 0.5988 (OUTLIER) cc_final: 0.5632 (m-30) REVERT: N 194 ASP cc_start: 0.7752 (t0) cc_final: 0.7387 (m-30) REVERT: N 350 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8815 (mt) REVERT: O 125 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6767 (mm-30) REVERT: O 149 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.6887 (mmtm) REVERT: O 195 ASP cc_start: 0.7598 (m-30) cc_final: 0.7376 (t0) REVERT: O 295 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8185 (mmtt) REVERT: O 350 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8671 (mt) REVERT: O 496 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7954 (pp20) REVERT: O 540 GLU cc_start: 0.8231 (mp0) cc_final: 0.7936 (pt0) REVERT: P 91 ASP cc_start: 0.7104 (t0) cc_final: 0.6814 (p0) REVERT: P 149 LYS cc_start: 0.7660 (mtmm) cc_final: 0.7385 (mtpp) REVERT: P 350 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8849 (mt) REVERT: Q 143 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.5591 (m-30) REVERT: Q 194 ASP cc_start: 0.7724 (t0) cc_final: 0.7361 (m-30) REVERT: Q 350 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8803 (mt) REVERT: R 125 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6691 (mm-30) REVERT: R 149 LYS cc_start: 0.7757 (mtpt) cc_final: 0.6925 (mmtm) REVERT: R 195 ASP cc_start: 0.7619 (m-30) cc_final: 0.7345 (t0) REVERT: R 350 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8664 (mt) REVERT: R 496 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8051 (pp20) outliers start: 303 outliers final: 225 residues processed: 980 average time/residue: 1.4623 time to fit residues: 1875.3103 Evaluate side-chains 1016 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 748 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 496 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 554 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 431 LYS Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 162 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 428 ASN Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 554 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 431 LYS Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 350 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 428 ASN Chi-restraints excluded: chain K residue 431 LYS Chi-restraints excluded: chain K residue 554 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 330 ASP Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 381 LEU Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 554 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 359 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 427 HIS Chi-restraints excluded: chain M residue 554 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 143 ASP Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 418 THR Chi-restraints excluded: chain N residue 428 ASN Chi-restraints excluded: chain N residue 433 GLU Chi-restraints excluded: chain N residue 485 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 554 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 149 LYS Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 295 LYS Chi-restraints excluded: chain O residue 350 LEU Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain O residue 496 GLU Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 350 LEU Chi-restraints excluded: chain P residue 359 VAL Chi-restraints excluded: chain P residue 381 LEU Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 427 HIS Chi-restraints excluded: chain P residue 554 VAL Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 190 ILE Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 350 LEU Chi-restraints excluded: chain Q residue 359 VAL Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 418 THR Chi-restraints excluded: chain Q residue 428 ASN Chi-restraints excluded: chain Q residue 485 GLU Chi-restraints excluded: chain Q residue 487 THR Chi-restraints excluded: chain Q residue 554 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 350 LEU Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 410 VAL Chi-restraints excluded: chain R residue 496 GLU Chi-restraints excluded: chain R residue 554 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 342 optimal weight: 20.0000 chunk 456 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 201 optimal weight: 30.0000 chunk 168 optimal weight: 0.0870 chunk 173 optimal weight: 5.9990 chunk 435 optimal weight: 3.9990 chunk 672 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 428 ASN C 151 HIS D 151 HIS E 131 ASN F 151 HIS M 47 ASN O 111 ASN P 47 ASN R 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.126251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102110 restraints weight = 76100.542| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.12 r_work: 0.2794 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 69552 Z= 0.234 Angle : 0.589 14.061 94626 Z= 0.308 Chirality : 0.048 0.146 10098 Planarity : 0.004 0.055 12816 Dihedral : 4.469 17.621 9486 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.78 % Allowed : 15.35 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.10 (0.09), residues: 8694 helix: 1.07 (0.11), residues: 2304 sheet: 0.78 (0.12), residues: 1746 loop : -1.01 (0.08), residues: 4644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 456 HIS 0.016 0.002 HIS D 151 PHE 0.010 0.001 PHE A 478 TYR 0.015 0.002 TYR M 375 ARG 0.006 0.000 ARG G 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17388 Ramachandran restraints generated. 8694 Oldfield, 0 Emsley, 8694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 757 time to evaluate : 5.875 Fit side-chains REVERT: A 3 GLU cc_start: 0.8301 (pt0) cc_final: 0.7469 (mm-30) REVERT: A 15 GLN cc_start: 0.8638 (mt0) cc_final: 0.8222 (tt0) REVERT: A 111 ASN cc_start: 0.8501 (t0) cc_final: 0.8175 (t0) REVERT: A 183 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: A 306 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8170 (mtp85) REVERT: A 350 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8742 (mt) REVERT: A 363 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7659 (tp30) REVERT: A 386 ASN cc_start: 0.8317 (m-40) cc_final: 0.7950 (m110) REVERT: B 107 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: B 191 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: B 427 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7687 (m90) REVERT: B 551 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8606 (mm-30) REVERT: C 107 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: C 111 ASN cc_start: 0.8257 (t0) cc_final: 0.7968 (t0) REVERT: C 154 ARG cc_start: 0.7751 (mmt90) cc_final: 0.7305 (ttm-80) REVERT: C 183 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: C 363 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7859 (tp30) REVERT: C 496 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7778 (pp20) REVERT: D 15 GLN cc_start: 0.8598 (mt0) cc_final: 0.8184 (tt0) REVERT: D 111 ASN cc_start: 0.8507 (t0) cc_final: 0.8202 (t0) REVERT: D 183 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: D 195 ASP cc_start: 0.7784 (m-30) cc_final: 0.7446 (m-30) REVERT: D 306 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8169 (mtp85) REVERT: D 350 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8740 (mt) REVERT: D 363 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7624 (tp30) REVERT: D 386 ASN cc_start: 0.8281 (m-40) cc_final: 0.7928 (m110) REVERT: D 496 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: E 107 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: E 182 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8905 (tp) REVERT: E 191 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: E 551 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8599 (mm-30) REVERT: F 3 GLU cc_start: 0.8260 (pt0) cc_final: 0.7556 (mm-30) REVERT: F 52 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: F 107 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: F 111 ASN cc_start: 0.8231 (t0) cc_final: 0.7951 (t0) REVERT: F 183 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8108 (mm-30) REVERT: F 363 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7890 (tp30) REVERT: F 496 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7778 (pp20) REVERT: G 195 ASP cc_start: 0.7416 (m-30) cc_final: 0.7121 (m-30) REVERT: G 431 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8316 (tttm) REVERT: H 162 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7517 (tp30) REVERT: H 169 SER cc_start: 0.9176 (OUTLIER) cc_final: 0.8861 (p) REVERT: H 183 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8128 (mm-30) REVERT: I 3 GLU cc_start: 0.8236 (pt0) cc_final: 0.7702 (mm-30) REVERT: I 13 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8277 (mt-10) REVERT: I 91 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: I 162 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: I 183 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: I 191 GLU cc_start: 0.8287 (tt0) cc_final: 0.7941 (tp30) REVERT: I 350 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8960 (mt) REVERT: J 171 ASP cc_start: 0.7514 (t0) cc_final: 0.7120 (t0) REVERT: J 192 TYR cc_start: 0.8732 (t80) cc_final: 0.8492 (t80) REVERT: J 431 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8340 (tttm) REVERT: J 567 ILE cc_start: 0.9281 (mt) cc_final: 0.9051 (mm) REVERT: K 107 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: K 162 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: K 183 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: L 3 GLU cc_start: 0.8265 (pt0) cc_final: 0.7714 (mm-30) REVERT: L 13 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8286 (mt-10) REVERT: L 91 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6544 (m-30) REVERT: L 162 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: L 183 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8151 (mm-30) REVERT: L 350 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8947 (mt) REVERT: L 363 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7645 (tp30) REVERT: M 91 ASP cc_start: 0.7270 (t0) cc_final: 0.6937 (p0) REVERT: M 350 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8851 (mt) REVERT: N 143 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5644 (m-30) REVERT: N 162 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: N 194 ASP cc_start: 0.7739 (t0) cc_final: 0.7374 (m-30) REVERT: N 350 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8816 (mt) REVERT: O 125 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6709 (mm-30) REVERT: O 149 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6876 (mmtm) REVERT: O 195 ASP cc_start: 0.7647 (m-30) cc_final: 0.7405 (t0) REVERT: O 295 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8186 (mmtt) REVERT: O 350 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8660 (mt) REVERT: O 496 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7920 (pp20) REVERT: O 540 GLU cc_start: 0.8256 (mp0) cc_final: 0.7913 (pt0) REVERT: P 91 ASP cc_start: 0.7132 (t0) cc_final: 0.6830 (p0) REVERT: P 149 LYS cc_start: 0.7646 (mtmm) cc_final: 0.7374 (mtpp) REVERT: P 350 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8845 (mt) REVERT: Q 143 ASP cc_start: 0.5984 (OUTLIER) cc_final: 0.5604 (m-30) REVERT: Q 151 HIS cc_start: 0.7109 (p-80) cc_final: 0.6812 (p90) REVERT: Q 162 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: Q 194 ASP cc_start: 0.7734 (t0) cc_final: 0.7365 (m-30) REVERT: Q 350 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8806 (mt) REVERT: R 125 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6683 (mm-30) REVERT: R 149 LYS cc_start: 0.7619 (mtpt) cc_final: 0.6839 (mmtm) REVERT: R 195 ASP cc_start: 0.7606 (m-30) cc_final: 0.7319 (t0) REVERT: R 350 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8668 (mt) REVERT: R 496 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8041 (pp20) outliers start: 279 outliers final: 216 residues processed: 968 average time/residue: 1.4628 time to fit residues: 1842.5331 Evaluate side-chains 1005 residues out of total 7380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 742 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 397 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 496 GLU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 386 ASN Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 496 GLU Chi-restraints excluded: chain F residue 554 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 431 LYS Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 162 GLU Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 423 VAL Chi-restraints excluded: chain H residue 428 ASN Chi-restraints excluded: chain H residue 431 LYS Chi-restraints excluded: chain H residue 554 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 320 MET Chi-restraints excluded: chain I residue 350 LEU Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 554 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 350 LEU Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 431 LYS Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain K residue 162 GLU Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 350 LEU Chi-restraints excluded: chain K residue 384 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 428 ASN Chi-restraints excluded: chain K residue 431 LYS Chi-restraints excluded: chain K residue 554 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 330 ASP Chi-restraints excluded: chain L residue 350 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 381 LEU Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 554 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 359 VAL Chi-restraints excluded: chain M residue 381 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 427 HIS Chi-restraints excluded: chain M residue 554 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 143 ASP Chi-restraints excluded: chain N residue 162 GLU Chi-restraints excluded: chain N residue 182 LEU Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 381 LEU Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 418 THR Chi-restraints excluded: chain N residue 428 ASN Chi-restraints excluded: chain N residue 433 GLU Chi-restraints excluded: chain N residue 485 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 554 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 149 LYS Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 295 LYS Chi-restraints excluded: chain O residue 350 LEU Chi-restraints excluded: chain O residue 359 VAL Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 384 VAL Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain O residue 496 GLU Chi-restraints excluded: chain O residue 554 VAL Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 350 LEU Chi-restraints excluded: chain P residue 359 VAL Chi-restraints excluded: chain P residue 381 LEU Chi-restraints excluded: chain P residue 384 VAL Chi-restraints excluded: chain P residue 427 HIS Chi-restraints excluded: chain P residue 554 VAL Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain Q residue 162 GLU Chi-restraints excluded: chain Q residue 182 LEU Chi-restraints excluded: chain Q residue 195 ASP Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 350 LEU Chi-restraints excluded: chain Q residue 359 VAL Chi-restraints excluded: chain Q residue 381 LEU Chi-restraints excluded: chain Q residue 384 VAL Chi-restraints excluded: chain Q residue 418 THR Chi-restraints excluded: chain Q residue 428 ASN Chi-restraints excluded: chain Q residue 485 GLU Chi-restraints excluded: chain Q residue 487 THR Chi-restraints excluded: chain Q residue 554 VAL Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 350 LEU Chi-restraints excluded: chain R residue 359 VAL Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 410 VAL Chi-restraints excluded: chain R residue 496 GLU Chi-restraints excluded: chain R residue 554 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 441 optimal weight: 30.0000 chunk 863 optimal weight: 0.9990 chunk 706 optimal weight: 20.0000 chunk 328 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 826 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 694 optimal weight: 5.9990 chunk 531 optimal weight: 4.9990 chunk 625 optimal weight: 10.0000 chunk 770 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS B 428 ASN C 151 HIS D 151 HIS E 131 ASN F 151 HIS M 47 ASN O 111 ASN P 47 ASN R 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.124754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.100264 restraints weight = 76066.741| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.17 r_work: 0.2777 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 69552 Z= 0.306 Angle : 0.646 16.442 94626 Z= 0.339 Chirality : 0.050 0.182 10098 Planarity : 0.005 0.055 12816 Dihedral : 4.676 18.609 9486 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.07 % Allowed : 15.19 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.15 (0.08), residues: 8694 helix: 0.94 (0.11), residues: 2304 sheet: 0.97 (0.12), residues: 1548 loop : -1.00 (0.08), residues: 4842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 489 HIS 0.006 0.002 HIS L 396 PHE 0.012 0.002 PHE A 478 TYR 0.016 0.002 TYR P 375 ARG 0.008 0.000 ARG F 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45171.48 seconds wall clock time: 770 minutes 35.21 seconds (46235.21 seconds total)