Starting phenix.real_space_refine on Wed Nov 20 14:03:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/11_2024/5wq7_6675_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/11_2024/5wq7_6675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/11_2024/5wq7_6675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/11_2024/5wq7_6675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/11_2024/5wq7_6675_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wq7_6675/11_2024/5wq7_6675_neut.cif" } resolution = 3.04 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= 0.000 sd= 0.005 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 75 5.16 5 C 34185 2.51 5 N 9420 2.21 5 O 10800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54480 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3632 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 455} Chain breaks: 3 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N Time building chain proxies: 13.37, per 1000 atoms: 0.25 Number of scatterers: 54480 At special positions: 0 Unit cell: (162.36, 161.04, 192.72, 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 75 16.00 O 10800 8.00 N 9420 7.00 C 34185 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: 13.11 Conformation dependent library (CDL) restraints added in 6.7 seconds 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13230 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 48 sheets defined 31.6% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.27 Creating SS restraints... Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP A 116 " --> pdb=" O PRO A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 147 through 164 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP B 116 " --> pdb=" O PRO B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 147 through 164 Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 584 " --> pdb=" O LEU B 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP C 116 " --> pdb=" O PRO C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 113 through 116' Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 178 through 188 removed outlier: 3.737A pdb=" N LEU C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 235 Processing helix chain 'C' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 377 Processing helix chain 'C' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 545 through 550 Processing helix chain 'C' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 579 " --> pdb=" O ASP C 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 116 removed outlier: 3.748A pdb=" N ASP D 116 " --> pdb=" O PRO D 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 113 through 116' Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 147 through 164 Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 235 Processing helix chain 'D' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 543 Processing helix chain 'D' and resid 545 through 550 Processing helix chain 'D' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D 579 " --> pdb=" O ASP D 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP E 116 " --> pdb=" O PRO E 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 113 through 116' Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 147 through 164 Processing helix chain 'E' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 235 Processing helix chain 'E' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 261 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 265 " --> pdb=" O VAL E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 377 Processing helix chain 'E' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 543 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER E 579 " --> pdb=" O ASP E 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS E 584 " --> pdb=" O LEU E 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP F 116 " --> pdb=" O PRO F 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 113 through 116' Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 147 through 164 Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU F 182 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 235 Processing helix chain 'F' and resid 254 through 267 removed outlier: 3.654A pdb=" N GLU F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 261 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 265 " --> pdb=" O VAL F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 377 Processing helix chain 'F' and resid 385 through 391 removed outlier: 3.551A pdb=" N ALA F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 543 Processing helix chain 'F' and resid 545 through 550 Processing helix chain 'F' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR F 577 " --> pdb=" O ASP F 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER F 579 " --> pdb=" O ASP F 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS F 584 " --> pdb=" O LEU F 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP G 116 " --> pdb=" O PRO G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 113 through 116' Processing helix chain 'G' and resid 117 through 126 Processing helix chain 'G' and resid 147 through 164 Processing helix chain 'G' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU G 182 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 235 Processing helix chain 'G' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL G 261 " --> pdb=" O ASN G 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL G 265 " --> pdb=" O VAL G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR G 313 " --> pdb=" O GLU G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 377 Processing helix chain 'G' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA G 391 " --> pdb=" O ASP G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 543 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR G 577 " --> pdb=" O ASP G 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER G 579 " --> pdb=" O ASP G 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS G 584 " --> pdb=" O LEU G 580 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP H 116 " --> pdb=" O PRO H 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 116' Processing helix chain 'H' and resid 117 through 126 Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU H 182 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN H 188 " --> pdb=" O GLU H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 235 Processing helix chain 'H' and resid 254 through 267 removed outlier: 3.654A pdb=" N GLU H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL H 261 " --> pdb=" O ASN H 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY H 264 " --> pdb=" O GLU H 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL H 265 " --> pdb=" O VAL H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR H 313 " --> pdb=" O GLU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 377 Processing helix chain 'H' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA H 391 " --> pdb=" O ASP H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 543 Processing helix chain 'H' and resid 545 through 550 Processing helix chain 'H' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR H 577 " --> pdb=" O ASP H 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER H 579 " --> pdb=" O ASP H 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS H 584 " --> pdb=" O LEU H 580 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP I 116 " --> pdb=" O PRO I 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 113 through 116' Processing helix chain 'I' and resid 117 through 126 Processing helix chain 'I' and resid 147 through 164 Processing helix chain 'I' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU I 182 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 235 Processing helix chain 'I' and resid 254 through 267 removed outlier: 3.654A pdb=" N GLU I 260 " --> pdb=" O THR I 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL I 261 " --> pdb=" O ASN I 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL I 265 " --> pdb=" O VAL I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR I 313 " --> pdb=" O GLU I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 377 Processing helix chain 'I' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA I 391 " --> pdb=" O ASP I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 543 Processing helix chain 'I' and resid 545 through 550 Processing helix chain 'I' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR I 577 " --> pdb=" O ASP I 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER I 579 " --> pdb=" O ASP I 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS I 584 " --> pdb=" O LEU I 580 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP J 116 " --> pdb=" O PRO J 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 113 through 116' Processing helix chain 'J' and resid 117 through 126 Processing helix chain 'J' and resid 147 through 164 Processing helix chain 'J' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU J 182 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 235 Processing helix chain 'J' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU J 260 " --> pdb=" O THR J 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 261 " --> pdb=" O ASN J 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL J 265 " --> pdb=" O VAL J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR J 313 " --> pdb=" O GLU J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 377 Processing helix chain 'J' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA J 391 " --> pdb=" O ASP J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 539 through 543 Processing helix chain 'J' and resid 545 through 550 Processing helix chain 'J' and resid 573 through 599 removed outlier: 3.572A pdb=" N TYR J 577 " --> pdb=" O ASP J 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER J 579 " --> pdb=" O ASP J 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS J 584 " --> pdb=" O LEU J 580 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP K 116 " --> pdb=" O PRO K 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 113 through 116' Processing helix chain 'K' and resid 117 through 126 Processing helix chain 'K' and resid 147 through 164 Processing helix chain 'K' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU K 182 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 235 Processing helix chain 'K' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL K 261 " --> pdb=" O ASN K 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY K 264 " --> pdb=" O GLU K 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL K 265 " --> pdb=" O VAL K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 377 Processing helix chain 'K' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA K 391 " --> pdb=" O ASP K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 543 Processing helix chain 'K' and resid 545 through 550 Processing helix chain 'K' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR K 577 " --> pdb=" O ASP K 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER K 579 " --> pdb=" O ASP K 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS K 584 " --> pdb=" O LEU K 580 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 116 removed outlier: 3.748A pdb=" N ASP L 116 " --> pdb=" O PRO L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 113 through 116' Processing helix chain 'L' and resid 117 through 126 Processing helix chain 'L' and resid 147 through 164 Processing helix chain 'L' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU L 182 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 235 Processing helix chain 'L' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL L 261 " --> pdb=" O ASN L 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL L 265 " --> pdb=" O VAL L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR L 313 " --> pdb=" O GLU L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 377 Processing helix chain 'L' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA L 391 " --> pdb=" O ASP L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 539 through 543 Processing helix chain 'L' and resid 545 through 550 Processing helix chain 'L' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR L 577 " --> pdb=" O ASP L 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 579 " --> pdb=" O ASP L 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS L 584 " --> pdb=" O LEU L 580 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP M 116 " --> pdb=" O PRO M 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 113 through 116' Processing helix chain 'M' and resid 117 through 126 Processing helix chain 'M' and resid 147 through 164 Processing helix chain 'M' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU M 182 " --> pdb=" O SER M 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN M 188 " --> pdb=" O GLU M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 235 Processing helix chain 'M' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU M 260 " --> pdb=" O THR M 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL M 261 " --> pdb=" O ASN M 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY M 264 " --> pdb=" O GLU M 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL M 265 " --> pdb=" O VAL M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR M 313 " --> pdb=" O GLU M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 377 Processing helix chain 'M' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA M 391 " --> pdb=" O ASP M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 539 through 543 Processing helix chain 'M' and resid 545 through 550 Processing helix chain 'M' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR M 577 " --> pdb=" O ASP M 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER M 579 " --> pdb=" O ASP M 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS M 584 " --> pdb=" O LEU M 580 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 116 removed outlier: 3.748A pdb=" N ASP N 116 " --> pdb=" O PRO N 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 113 through 116' Processing helix chain 'N' and resid 117 through 126 Processing helix chain 'N' and resid 147 through 164 Processing helix chain 'N' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU N 182 " --> pdb=" O SER N 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN N 188 " --> pdb=" O GLU N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 235 Processing helix chain 'N' and resid 254 through 267 removed outlier: 3.653A pdb=" N GLU N 260 " --> pdb=" O THR N 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL N 261 " --> pdb=" O ASN N 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY N 264 " --> pdb=" O GLU N 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL N 265 " --> pdb=" O VAL N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR N 313 " --> pdb=" O GLU N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 377 Processing helix chain 'N' and resid 385 through 391 removed outlier: 3.550A pdb=" N ALA N 391 " --> pdb=" O ASP N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 539 through 543 Processing helix chain 'N' and resid 545 through 550 Processing helix chain 'N' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR N 577 " --> pdb=" O ASP N 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER N 579 " --> pdb=" O ASP N 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS N 584 " --> pdb=" O LEU N 580 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 116 removed outlier: 3.749A pdb=" N ASP O 116 " --> pdb=" O PRO O 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 113 through 116' Processing helix chain 'O' and resid 117 through 126 Processing helix chain 'O' and resid 147 through 164 Processing helix chain 'O' and resid 178 through 188 removed outlier: 3.736A pdb=" N LEU O 182 " --> pdb=" O SER O 178 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN O 188 " --> pdb=" O GLU O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 235 Processing helix chain 'O' and resid 254 through 267 removed outlier: 3.654A pdb=" N GLU O 260 " --> pdb=" O THR O 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 261 " --> pdb=" O ASN O 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY O 264 " --> pdb=" O GLU O 260 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL O 265 " --> pdb=" O VAL O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 319 removed outlier: 3.768A pdb=" N THR O 313 " --> pdb=" O GLU O 309 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 377 Processing helix chain 'O' and resid 385 through 391 removed outlier: 3.551A pdb=" N ALA O 391 " --> pdb=" O ASP O 387 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 543 Processing helix chain 'O' and resid 545 through 550 Processing helix chain 'O' and resid 573 through 599 removed outlier: 3.573A pdb=" N TYR O 577 " --> pdb=" O ASP O 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER O 579 " --> pdb=" O ASP O 575 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS O 584 " --> pdb=" O LEU O 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 108 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 173 Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 249 Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 348 removed outlier: 3.571A pdb=" N ARG A 557 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 566 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL A 521 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 16.518A pdb=" N VAL A 520 " --> pdb=" O LEU O 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU O 428 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 522 " --> pdb=" O VAL O 426 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP O 346 " --> pdb=" O GLN O 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP N 346 " --> pdb=" O GLN N 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP M 346 " --> pdb=" O GLN M 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP L 346 " --> pdb=" O GLN L 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP K 346 " --> pdb=" O GLN K 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP J 346 " --> pdb=" O GLN J 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP I 346 " --> pdb=" O GLN I 354 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP H 346 " --> pdb=" O GLN H 354 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP G 346 " --> pdb=" O GLN G 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP F 346 " --> pdb=" O GLN F 354 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 346 " --> pdb=" O GLN E 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP D 346 " --> pdb=" O GLN D 354 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 346 " --> pdb=" O GLN C 354 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 346 " --> pdb=" O GLN B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 348 removed outlier: 3.522A pdb=" N TRP A 346 " --> pdb=" O GLN A 354 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG O 557 " --> pdb=" O ASN O 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE O 566 " --> pdb=" O VAL O 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL O 521 " --> pdb=" O ILE O 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL O 520 " --> pdb=" O LEU N 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU N 428 " --> pdb=" O VAL O 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU O 522 " --> pdb=" O VAL N 426 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG N 557 " --> pdb=" O ASN N 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE N 566 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL N 521 " --> pdb=" O ILE N 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL N 520 " --> pdb=" O LEU M 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU M 428 " --> pdb=" O VAL N 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU N 522 " --> pdb=" O VAL M 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG M 557 " --> pdb=" O ASN M 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE M 566 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL M 521 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 16.518A pdb=" N VAL M 520 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU L 428 " --> pdb=" O VAL M 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU M 522 " --> pdb=" O VAL L 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG L 557 " --> pdb=" O ASN L 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE L 566 " --> pdb=" O VAL L 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL L 521 " --> pdb=" O ILE L 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL L 520 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU K 428 " --> pdb=" O VAL L 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU L 522 " --> pdb=" O VAL K 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG K 557 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE K 566 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL K 521 " --> pdb=" O ILE K 566 " (cutoff:3.500A) removed outlier: 16.516A pdb=" N VAL K 520 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU J 428 " --> pdb=" O VAL K 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU K 522 " --> pdb=" O VAL J 426 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG J 557 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE J 566 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL J 521 " --> pdb=" O ILE J 566 " (cutoff:3.500A) removed outlier: 16.518A pdb=" N VAL J 520 " --> pdb=" O LEU I 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU I 428 " --> pdb=" O VAL J 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU J 522 " --> pdb=" O VAL I 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG I 557 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE I 566 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL I 521 " --> pdb=" O ILE I 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL I 520 " --> pdb=" O LEU H 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU H 428 " --> pdb=" O VAL I 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU I 522 " --> pdb=" O VAL H 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG H 557 " --> pdb=" O ASN H 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE H 566 " --> pdb=" O VAL H 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL H 521 " --> pdb=" O ILE H 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL H 520 " --> pdb=" O LEU G 428 " (cutoff:3.500A) removed outlier: 12.659A pdb=" N LEU G 428 " --> pdb=" O VAL H 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU H 522 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG G 557 " --> pdb=" O ASN G 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE G 566 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL G 521 " --> pdb=" O ILE G 566 " (cutoff:3.500A) removed outlier: 16.516A pdb=" N VAL G 520 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU F 428 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU G 522 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 557 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 566 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL F 521 " --> pdb=" O ILE F 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL F 520 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU E 428 " --> pdb=" O VAL F 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU F 522 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 557 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE E 566 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL E 521 " --> pdb=" O ILE E 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL E 520 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU D 428 " --> pdb=" O VAL E 520 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 522 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 557 " --> pdb=" O ASN D 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE D 566 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL D 521 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 16.516A pdb=" N VAL D 520 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU C 428 " --> pdb=" O VAL D 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU D 522 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 557 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 566 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL C 521 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL C 520 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU B 428 " --> pdb=" O VAL C 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 522 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 557 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 566 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL B 521 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 16.517A pdb=" N VAL B 520 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 12.658A pdb=" N LEU A 428 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 522 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 433 through 443 removed outlier: 12.674A pdb=" N THR A 463 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL A 491 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR O 463 " --> pdb=" O VAL O 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL O 491 " --> pdb=" O THR O 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR N 463 " --> pdb=" O VAL N 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL N 491 " --> pdb=" O THR N 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR M 463 " --> pdb=" O VAL M 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL M 491 " --> pdb=" O THR M 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR L 463 " --> pdb=" O VAL L 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL L 491 " --> pdb=" O THR L 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR K 463 " --> pdb=" O VAL K 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL K 491 " --> pdb=" O THR K 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR J 463 " --> pdb=" O VAL J 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL J 491 " --> pdb=" O THR J 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR I 463 " --> pdb=" O VAL I 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL I 491 " --> pdb=" O THR I 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR H 463 " --> pdb=" O VAL H 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL H 491 " --> pdb=" O THR H 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR G 463 " --> pdb=" O VAL G 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL G 491 " --> pdb=" O THR G 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR F 463 " --> pdb=" O VAL F 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL F 491 " --> pdb=" O THR F 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR E 463 " --> pdb=" O VAL E 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL E 491 " --> pdb=" O THR E 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR D 463 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL D 491 " --> pdb=" O THR D 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR C 463 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL C 491 " --> pdb=" O THR C 463 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N THR B 463 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL B 491 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 108 Processing sheet with id=AA8, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA9, first strand: chain 'B' and resid 245 through 249 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 108 Processing sheet with id=AB2, first strand: chain 'C' and resid 170 through 173 Processing sheet with id=AB3, first strand: chain 'C' and resid 245 through 249 Processing sheet with id=AB4, first strand: chain 'D' and resid 103 through 108 Processing sheet with id=AB5, first strand: chain 'D' and resid 170 through 173 Processing sheet with id=AB6, first strand: chain 'D' and resid 245 through 249 Processing sheet with id=AB7, first strand: chain 'E' and resid 103 through 108 Processing sheet with id=AB8, first strand: chain 'E' and resid 170 through 173 Processing sheet with id=AB9, first strand: chain 'E' and resid 245 through 249 Processing sheet with id=AC1, first strand: chain 'F' and resid 103 through 108 Processing sheet with id=AC2, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AC3, first strand: chain 'F' and resid 245 through 249 Processing sheet with id=AC4, first strand: chain 'G' and resid 103 through 108 Processing sheet with id=AC5, first strand: chain 'G' and resid 170 through 173 Processing sheet with id=AC6, first strand: chain 'G' and resid 245 through 249 Processing sheet with id=AC7, first strand: chain 'H' and resid 103 through 108 Processing sheet with id=AC8, first strand: chain 'H' and resid 170 through 173 Processing sheet with id=AC9, first strand: chain 'H' and resid 245 through 249 Processing sheet with id=AD1, first strand: chain 'I' and resid 103 through 108 Processing sheet with id=AD2, first strand: chain 'I' and resid 170 through 173 Processing sheet with id=AD3, first strand: chain 'I' and resid 245 through 249 Processing sheet with id=AD4, first strand: chain 'J' and resid 103 through 108 Processing sheet with id=AD5, first strand: chain 'J' and resid 170 through 173 Processing sheet with id=AD6, first strand: chain 'J' and resid 245 through 249 Processing sheet with id=AD7, first strand: chain 'K' and resid 103 through 108 Processing sheet with id=AD8, first strand: chain 'K' and resid 170 through 173 Processing sheet with id=AD9, first strand: chain 'K' and resid 245 through 249 Processing sheet with id=AE1, first strand: chain 'L' and resid 103 through 108 Processing sheet with id=AE2, first strand: chain 'L' and resid 170 through 173 Processing sheet with id=AE3, first strand: chain 'L' and resid 245 through 249 Processing sheet with id=AE4, first strand: chain 'M' and resid 103 through 108 Processing sheet with id=AE5, first strand: chain 'M' and resid 170 through 173 Processing sheet with id=AE6, first strand: chain 'M' and resid 245 through 249 Processing sheet with id=AE7, first strand: chain 'N' and resid 103 through 108 Processing sheet with id=AE8, first strand: chain 'N' and resid 170 through 173 Processing sheet with id=AE9, first strand: chain 'N' and resid 245 through 249 Processing sheet with id=AF1, first strand: chain 'O' and resid 103 through 108 Processing sheet with id=AF2, first strand: chain 'O' and resid 170 through 173 Processing sheet with id=AF3, first strand: chain 'O' and resid 245 through 249 4005 hydrogen bonds defined for protein. 11160 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: 27.81 Time building geometry restraints manager: 15.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9675 1.31 - 1.44: 12615 1.44 - 1.56: 32655 1.56 - 1.68: 0 1.68 - 1.80: 150 Bond restraints: 55095 Sorted by residual: bond pdb=" C GLN L 345 " pdb=" O GLN L 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.38e+01 bond pdb=" C GLN I 345 " pdb=" O GLN I 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.38e+01 bond pdb=" C GLN J 345 " pdb=" O GLN J 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.37e+01 bond pdb=" C GLN H 345 " pdb=" O GLN H 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.37e+01 bond pdb=" C GLN G 345 " pdb=" O GLN G 345 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.14e-02 7.69e+03 1.37e+01 ... (remaining 55090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 71246 2.14 - 4.27: 3002 4.27 - 6.41: 377 6.41 - 8.55: 45 8.55 - 10.68: 75 Bond angle restraints: 74745 Sorted by residual: angle pdb=" C SER H 266 " pdb=" CA SER H 266 " pdb=" CB SER H 266 " ideal model delta sigma weight residual 110.38 99.70 10.68 2.04e+00 2.40e-01 2.74e+01 angle pdb=" C SER L 266 " pdb=" CA SER L 266 " pdb=" CB SER L 266 " ideal model delta sigma weight residual 110.38 99.70 10.68 2.04e+00 2.40e-01 2.74e+01 angle pdb=" C SER B 266 " pdb=" CA SER B 266 " pdb=" CB SER B 266 " ideal model delta sigma weight residual 110.38 99.73 10.65 2.04e+00 2.40e-01 2.73e+01 angle pdb=" C SER D 266 " pdb=" CA SER D 266 " pdb=" CB SER D 266 " ideal model delta sigma weight residual 110.38 99.73 10.65 2.04e+00 2.40e-01 2.72e+01 angle pdb=" C SER O 266 " pdb=" CA SER O 266 " pdb=" CB SER O 266 " ideal model delta sigma weight residual 110.38 99.74 10.64 2.04e+00 2.40e-01 2.72e+01 ... (remaining 74740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 31770 16.55 - 33.10: 1500 33.10 - 49.65: 375 49.65 - 66.20: 75 66.20 - 82.75: 60 Dihedral angle restraints: 33780 sinusoidal: 13365 harmonic: 20415 Sorted by residual: dihedral pdb=" CA THR E 166 " pdb=" C THR E 166 " pdb=" N GLU E 167 " pdb=" CA GLU E 167 " ideal model delta harmonic sigma weight residual 180.00 145.89 34.11 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA THR F 166 " pdb=" C THR F 166 " pdb=" N GLU F 167 " pdb=" CA GLU F 167 " ideal model delta harmonic sigma weight residual 180.00 145.89 34.11 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA THR J 166 " pdb=" C THR J 166 " pdb=" N GLU J 167 " pdb=" CA GLU J 167 " ideal model delta harmonic sigma weight residual 180.00 145.91 34.09 0 5.00e+00 4.00e-02 4.65e+01 ... (remaining 33777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 6794 0.063 - 0.126: 1853 0.126 - 0.189: 376 0.189 - 0.252: 37 0.252 - 0.315: 30 Chirality restraints: 9090 Sorted by residual: chirality pdb=" CA SER D 266 " pdb=" N SER D 266 " pdb=" C SER D 266 " pdb=" CB SER D 266 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA SER H 266 " pdb=" N SER H 266 " pdb=" C SER H 266 " pdb=" CB SER H 266 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA SER E 266 " pdb=" N SER E 266 " pdb=" C SER E 266 " pdb=" CB SER E 266 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 9087 not shown) Planarity restraints: 9690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 577 " 0.032 2.00e-02 2.50e+03 2.64e-02 1.39e+01 pdb=" CG TYR O 577 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR O 577 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR O 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR O 577 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 577 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR O 577 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR O 577 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 577 " 0.032 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR F 577 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR F 577 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR F 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 577 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR F 577 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR F 577 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 577 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 577 " 0.032 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR M 577 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR M 577 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR M 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR M 577 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR M 577 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR M 577 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR M 577 " 0.001 2.00e-02 2.50e+03 ... (remaining 9687 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 420 2.50 - 3.10: 42387 3.10 - 3.70: 80650 3.70 - 4.30: 120255 4.30 - 4.90: 205906 Nonbonded interactions: 449618 Sorted by model distance: nonbonded pdb=" OE1 GLU M 333 " pdb=" NH1 ARG M 506 " model vdw 1.901 3.120 nonbonded pdb=" OE1 GLU D 333 " pdb=" NH1 ARG D 506 " model vdw 1.901 3.120 nonbonded pdb=" OE1 GLU L 333 " pdb=" NH1 ARG L 506 " model vdw 1.901 3.120 nonbonded pdb=" OE1 GLU O 333 " pdb=" NH1 ARG O 506 " model vdw 1.901 3.120 nonbonded pdb=" OE1 GLU C 333 " pdb=" NH1 ARG C 506 " model vdw 1.901 3.120 ... (remaining 449613 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.100 Extract box with map and model: 1.900 Check model and map are aligned: 0.390 Set scattering table: 0.500 Process input model: 102.180 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.009 0.070 55095 Z= 0.559 Angle : 1.021 10.683 74745 Z= 0.578 Chirality : 0.062 0.315 9090 Planarity : 0.005 0.055 9690 Dihedral : 11.516 82.747 20550 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.09 % Favored : 95.26 % Rotamer: Outliers : 0.49 % Allowed : 2.72 % Favored : 96.79 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.95 (0.08), residues: 6960 helix: -3.23 (0.09), residues: 1950 sheet: -0.82 (0.08), residues: 3090 loop : -1.98 (0.11), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 386 HIS 0.006 0.003 HIS K 173 PHE 0.022 0.003 PHE O 503 TYR 0.063 0.004 TYR O 577 ARG 0.009 0.001 ARG M 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 869 time to evaluate : 5.887 Fit side-chains REVERT: A 295 GLN cc_start: 0.8737 (mm110) cc_final: 0.7803 (mt0) REVERT: A 310 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7334 (pttt) REVERT: A 373 TYR cc_start: 0.6719 (t80) cc_final: 0.6328 (t80) REVERT: A 542 ASP cc_start: 0.9144 (m-30) cc_final: 0.8859 (m-30) REVERT: A 556 GLU cc_start: 0.8498 (tt0) cc_final: 0.8254 (tt0) REVERT: A 575 ASP cc_start: 0.8562 (m-30) cc_final: 0.8204 (t0) REVERT: A 588 TYR cc_start: 0.8299 (t80) cc_final: 0.7639 (t80) REVERT: A 594 GLN cc_start: 0.7199 (tt0) cc_final: 0.6629 (tm-30) REVERT: B 295 GLN cc_start: 0.8648 (mm110) cc_final: 0.7576 (mt0) REVERT: B 395 MET cc_start: 0.8286 (ttp) cc_final: 0.8062 (ttp) REVERT: B 542 ASP cc_start: 0.8864 (m-30) cc_final: 0.8584 (m-30) REVERT: B 594 GLN cc_start: 0.7253 (tt0) cc_final: 0.6941 (tt0) REVERT: B 614 GLU cc_start: 0.7706 (tt0) cc_final: 0.7352 (tp30) REVERT: C 125 MET cc_start: 0.0479 (ttp) cc_final: 0.0197 (mmt) REVERT: C 295 GLN cc_start: 0.8493 (mm110) cc_final: 0.7512 (mt0) REVERT: C 310 LYS cc_start: 0.7334 (mtmt) cc_final: 0.6816 (pttt) REVERT: C 429 ASP cc_start: 0.8565 (p0) cc_final: 0.8331 (p0) REVERT: C 460 GLU cc_start: 0.8091 (tt0) cc_final: 0.7832 (tt0) REVERT: C 542 ASP cc_start: 0.9096 (m-30) cc_final: 0.8807 (m-30) REVERT: C 588 TYR cc_start: 0.8343 (t80) cc_final: 0.7362 (t80) REVERT: C 590 GLN cc_start: 0.7259 (mt0) cc_final: 0.6869 (pt0) REVERT: C 592 GLN cc_start: 0.6446 (mt0) cc_final: 0.6077 (mt0) REVERT: C 594 GLN cc_start: 0.7041 (tt0) cc_final: 0.6601 (tm-30) REVERT: C 614 GLU cc_start: 0.7598 (tt0) cc_final: 0.7112 (tp30) REVERT: D 295 GLN cc_start: 0.8672 (mm110) cc_final: 0.7580 (mt0) REVERT: D 309 GLU cc_start: 0.8278 (tp30) cc_final: 0.7926 (mm-30) REVERT: D 399 PHE cc_start: 0.6064 (m-80) cc_final: 0.5854 (m-80) REVERT: D 460 GLU cc_start: 0.7758 (tt0) cc_final: 0.7526 (tt0) REVERT: D 483 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8630 (mt-10) REVERT: D 556 GLU cc_start: 0.8773 (tt0) cc_final: 0.8570 (tt0) REVERT: D 563 MET cc_start: 0.9006 (mmt) cc_final: 0.8788 (mtp) REVERT: D 590 GLN cc_start: 0.7048 (mt0) cc_final: 0.6726 (tt0) REVERT: D 594 GLN cc_start: 0.7114 (tt0) cc_final: 0.6698 (tm-30) REVERT: E 125 MET cc_start: 0.0242 (ttp) cc_final: -0.0208 (mmt) REVERT: E 295 GLN cc_start: 0.8732 (mm110) cc_final: 0.7786 (mt0) REVERT: E 310 LYS cc_start: 0.7452 (mtmt) cc_final: 0.7075 (pttt) REVERT: E 373 TYR cc_start: 0.6723 (t80) cc_final: 0.6403 (t80) REVERT: E 418 ASP cc_start: 0.8741 (t0) cc_final: 0.8532 (t0) REVERT: E 440 ASP cc_start: 0.8969 (t70) cc_final: 0.8729 (t70) REVERT: E 487 GLU cc_start: 0.8340 (pt0) cc_final: 0.8112 (pt0) REVERT: E 542 ASP cc_start: 0.8788 (m-30) cc_final: 0.8426 (m-30) REVERT: E 590 GLN cc_start: 0.7137 (mt0) cc_final: 0.6714 (pt0) REVERT: E 594 GLN cc_start: 0.6984 (tt0) cc_final: 0.6485 (tm-30) REVERT: F 248 TYR cc_start: 0.7357 (m-80) cc_final: 0.7076 (m-80) REVERT: F 295 GLN cc_start: 0.8640 (mm110) cc_final: 0.7483 (mt0) REVERT: F 309 GLU cc_start: 0.7953 (tp30) cc_final: 0.7671 (mm-30) REVERT: F 374 LYS cc_start: 0.8075 (mttt) cc_final: 0.7871 (mptt) REVERT: F 542 ASP cc_start: 0.9041 (m-30) cc_final: 0.8602 (m-30) REVERT: F 575 ASP cc_start: 0.8603 (m-30) cc_final: 0.8285 (t0) REVERT: F 590 GLN cc_start: 0.7447 (mt0) cc_final: 0.7025 (pt0) REVERT: F 594 GLN cc_start: 0.7031 (tt0) cc_final: 0.6725 (tm-30) REVERT: G 310 LYS cc_start: 0.7361 (mtmt) cc_final: 0.6951 (pttt) REVERT: G 429 ASP cc_start: 0.8729 (p0) cc_final: 0.8341 (p0) REVERT: G 431 LYS cc_start: 0.8683 (tptp) cc_final: 0.8473 (tmtt) REVERT: G 460 GLU cc_start: 0.7785 (tt0) cc_final: 0.7546 (tt0) REVERT: G 483 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8507 (mt-10) REVERT: G 487 GLU cc_start: 0.8419 (pt0) cc_final: 0.8083 (pt0) REVERT: G 589 ARG cc_start: 0.6391 (ttt-90) cc_final: 0.6148 (ttt-90) REVERT: G 590 GLN cc_start: 0.7006 (mt0) cc_final: 0.6657 (pt0) REVERT: G 594 GLN cc_start: 0.7062 (tt0) cc_final: 0.6532 (tm-30) REVERT: H 248 TYR cc_start: 0.7387 (m-80) cc_final: 0.6938 (m-80) REVERT: H 295 GLN cc_start: 0.8712 (mm110) cc_final: 0.7818 (mt0) REVERT: H 395 MET cc_start: 0.8263 (ttp) cc_final: 0.7899 (ttp) REVERT: H 429 ASP cc_start: 0.8641 (p0) cc_final: 0.8374 (p0) REVERT: H 436 ASN cc_start: 0.8444 (m-40) cc_final: 0.8138 (t0) REVERT: H 509 GLN cc_start: 0.8535 (pt0) cc_final: 0.8259 (pp30) REVERT: H 590 GLN cc_start: 0.7361 (mt0) cc_final: 0.6781 (tm-30) REVERT: H 594 GLN cc_start: 0.7328 (tt0) cc_final: 0.6926 (tm-30) REVERT: I 262 LEU cc_start: 0.7906 (mt) cc_final: 0.7677 (mt) REVERT: I 295 GLN cc_start: 0.8614 (mm110) cc_final: 0.7431 (mt0) REVERT: I 309 GLU cc_start: 0.8007 (tp30) cc_final: 0.7786 (mm-30) REVERT: I 310 LYS cc_start: 0.7574 (mtmt) cc_final: 0.7163 (pttt) REVERT: I 373 TYR cc_start: 0.7027 (t80) cc_final: 0.6629 (t80) REVERT: I 460 GLU cc_start: 0.7922 (tt0) cc_final: 0.7601 (tt0) REVERT: I 483 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8696 (mt-10) REVERT: I 542 ASP cc_start: 0.8759 (m-30) cc_final: 0.8517 (m-30) REVERT: I 590 GLN cc_start: 0.7296 (mt0) cc_final: 0.6902 (pt0) REVERT: J 258 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7801 (tt) REVERT: J 295 GLN cc_start: 0.8527 (mm110) cc_final: 0.7542 (mt0) REVERT: J 310 LYS cc_start: 0.7203 (mtmt) cc_final: 0.6815 (pttt) REVERT: J 399 PHE cc_start: 0.6267 (m-80) cc_final: 0.5885 (m-80) REVERT: J 460 GLU cc_start: 0.8007 (tt0) cc_final: 0.7626 (mp0) REVERT: J 483 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8624 (mt-10) REVERT: J 509 GLN cc_start: 0.8528 (pt0) cc_final: 0.8312 (pp30) REVERT: J 594 GLN cc_start: 0.6973 (tt0) cc_final: 0.6556 (tm-30) REVERT: K 262 LEU cc_start: 0.7741 (mt) cc_final: 0.7395 (mt) REVERT: K 429 ASP cc_start: 0.8531 (p0) cc_final: 0.8214 (p0) REVERT: K 460 GLU cc_start: 0.7902 (tt0) cc_final: 0.7634 (tt0) REVERT: K 485 GLU cc_start: 0.8516 (tt0) cc_final: 0.8303 (tt0) REVERT: K 590 GLN cc_start: 0.7532 (mt0) cc_final: 0.7101 (pt0) REVERT: K 594 GLN cc_start: 0.7193 (tt0) cc_final: 0.6950 (tm-30) REVERT: L 295 GLN cc_start: 0.8778 (mm110) cc_final: 0.7871 (mt0) REVERT: L 483 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8699 (mt-10) REVERT: L 486 GLN cc_start: 0.8506 (pt0) cc_final: 0.8188 (pp30) REVERT: L 487 GLU cc_start: 0.8523 (pt0) cc_final: 0.8308 (pt0) REVERT: L 556 GLU cc_start: 0.8598 (tt0) cc_final: 0.8380 (tt0) REVERT: L 589 ARG cc_start: 0.5895 (ttt-90) cc_final: 0.5655 (ttp80) REVERT: L 590 GLN cc_start: 0.7030 (mt0) cc_final: 0.6626 (pt0) REVERT: L 594 GLN cc_start: 0.7043 (tt0) cc_final: 0.6756 (tt0) REVERT: M 248 TYR cc_start: 0.7289 (m-80) cc_final: 0.6432 (m-80) REVERT: M 262 LEU cc_start: 0.7799 (mt) cc_final: 0.7502 (mt) REVERT: M 295 GLN cc_start: 0.8737 (mm110) cc_final: 0.7727 (mt0) REVERT: M 309 GLU cc_start: 0.8044 (tp30) cc_final: 0.7830 (mm-30) REVERT: M 483 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8621 (mt-10) REVERT: M 560 ARG cc_start: 0.8573 (ttm170) cc_final: 0.8360 (ttp-170) REVERT: M 594 GLN cc_start: 0.6969 (tt0) cc_final: 0.6580 (tm-30) REVERT: N 248 TYR cc_start: 0.7129 (m-80) cc_final: 0.6851 (m-80) REVERT: N 295 GLN cc_start: 0.8775 (mm110) cc_final: 0.7824 (mt0) REVERT: N 310 LYS cc_start: 0.7403 (mtmt) cc_final: 0.6904 (pttt) REVERT: N 373 TYR cc_start: 0.6846 (t80) cc_final: 0.6540 (t80) REVERT: N 379 ILE cc_start: 0.9097 (mt) cc_final: 0.8822 (mp) REVERT: N 399 PHE cc_start: 0.6146 (m-80) cc_final: 0.5622 (m-80) REVERT: N 401 ASN cc_start: 0.6603 (t0) cc_final: 0.6363 (t0) REVERT: N 483 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8738 (mt-10) REVERT: N 575 ASP cc_start: 0.8669 (m-30) cc_final: 0.8448 (t0) REVERT: N 590 GLN cc_start: 0.7322 (mt0) cc_final: 0.6877 (tm-30) REVERT: N 594 GLN cc_start: 0.6934 (tt0) cc_final: 0.6576 (tm-30) REVERT: O 295 GLN cc_start: 0.8647 (mm110) cc_final: 0.7712 (mt0) REVERT: O 310 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7528 (pttt) REVERT: O 395 MET cc_start: 0.8458 (ttp) cc_final: 0.8133 (ttp) REVERT: O 401 ASN cc_start: 0.6576 (t0) cc_final: 0.6358 (t0) REVERT: O 418 ASP cc_start: 0.8280 (t0) cc_final: 0.8046 (t0) REVERT: O 460 GLU cc_start: 0.7954 (tt0) cc_final: 0.7746 (tt0) REVERT: O 483 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8691 (mt-10) REVERT: O 509 GLN cc_start: 0.8549 (pt0) cc_final: 0.8296 (pp30) REVERT: O 590 GLN cc_start: 0.7120 (mt0) cc_final: 0.6862 (tm-30) REVERT: O 594 GLN cc_start: 0.7111 (tt0) cc_final: 0.6673 (tm-30) outliers start: 30 outliers final: 22 residues processed: 892 average time/residue: 0.7039 time to fit residues: 1031.7253 Evaluate side-chains 639 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 616 time to evaluate : 6.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 349 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain G residue 349 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain I residue 349 LYS Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 349 LYS Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 349 LYS Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 349 LYS Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 349 LYS Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 349 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 595 optimal weight: 0.8980 chunk 534 optimal weight: 0.6980 chunk 296 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 360 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 552 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 336 optimal weight: 10.0000 chunk 411 optimal weight: 0.9980 chunk 640 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 335 GLN A 368 GLN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 295 GLN B 324 GLN B 335 GLN B 368 GLN B 436 ASN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN C 295 GLN C 308 GLN C 324 GLN C 335 GLN C 368 GLN C 436 ASN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN D 295 GLN D 308 GLN D 324 GLN D 335 GLN D 368 GLN D 436 ASN ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 295 GLN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN E 324 GLN E 335 GLN E 368 GLN ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN F 295 GLN F 308 GLN F 324 GLN F 335 GLN F 368 GLN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN G 295 GLN G 308 GLN G 324 GLN G 368 GLN ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 GLN H 295 GLN H 308 GLN H 324 GLN H 335 GLN H 368 GLN ** H 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 GLN ** I 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN I 295 GLN I 308 GLN I 324 GLN I 368 GLN ** I 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 188 GLN J 295 GLN J 308 GLN J 324 GLN J 335 GLN J 368 GLN J 475 ASN J 486 GLN ** K 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 GLN K 295 GLN K 308 GLN K 324 GLN K 335 GLN K 368 GLN ** K 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN L 295 GLN L 308 GLN L 324 GLN L 335 GLN L 368 GLN L 475 ASN ** M 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 295 GLN ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 324 GLN M 335 GLN M 368 GLN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN N 295 GLN N 308 GLN N 324 GLN N 335 GLN N 368 GLN ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 188 GLN O 295 GLN O 308 GLN O 324 GLN O 335 GLN O 368 GLN ** O 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 55095 Z= 0.255 Angle : 0.700 7.769 74745 Z= 0.374 Chirality : 0.049 0.186 9090 Planarity : 0.005 0.038 9690 Dihedral : 6.467 49.287 7600 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.08 % Favored : 97.70 % Rotamer: Outliers : 1.91 % Allowed : 6.77 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.43 (0.09), residues: 6960 helix: -1.21 (0.10), residues: 1890 sheet: -0.40 (0.08), residues: 3015 loop : -1.16 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 404 HIS 0.003 0.001 HIS K 135 PHE 0.011 0.002 PHE H 529 TYR 0.037 0.002 TYR M 577 ARG 0.011 0.001 ARG L 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 782 time to evaluate : 5.792 Fit side-chains REVERT: A 294 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 295 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8399 (mm-40) REVERT: A 302 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8097 (p) REVERT: A 310 LYS cc_start: 0.7525 (mtmt) cc_final: 0.7244 (pttt) REVERT: A 374 LYS cc_start: 0.7843 (mttt) cc_final: 0.7633 (mptt) REVERT: A 542 ASP cc_start: 0.8910 (m-30) cc_final: 0.8642 (m-30) REVERT: A 575 ASP cc_start: 0.8604 (m-30) cc_final: 0.8358 (t0) REVERT: A 588 TYR cc_start: 0.8149 (t80) cc_final: 0.7509 (t80) REVERT: A 594 GLN cc_start: 0.7385 (tt0) cc_final: 0.7155 (tt0) REVERT: B 295 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8493 (mm-40) REVERT: B 305 GLN cc_start: 0.6368 (tm-30) cc_final: 0.6156 (tm-30) REVERT: B 341 ASN cc_start: 0.7907 (p0) cc_final: 0.7628 (p0) REVERT: B 418 ASP cc_start: 0.8401 (t0) cc_final: 0.8076 (m-30) REVERT: B 542 ASP cc_start: 0.8702 (m-30) cc_final: 0.8439 (m-30) REVERT: B 575 ASP cc_start: 0.8508 (m-30) cc_final: 0.8188 (t0) REVERT: B 594 GLN cc_start: 0.7083 (tt0) cc_final: 0.6844 (tt0) REVERT: B 614 GLU cc_start: 0.7632 (tt0) cc_final: 0.7421 (tp30) REVERT: C 295 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8492 (mp10) REVERT: C 304 ASP cc_start: 0.5972 (p0) cc_final: 0.5683 (p0) REVERT: C 310 LYS cc_start: 0.7215 (mtmt) cc_final: 0.6907 (pttt) REVERT: C 429 ASP cc_start: 0.8572 (p0) cc_final: 0.8255 (p0) REVERT: C 460 GLU cc_start: 0.8328 (tt0) cc_final: 0.8078 (tt0) REVERT: C 478 ASP cc_start: 0.8116 (m-30) cc_final: 0.7275 (p0) REVERT: C 527 ASP cc_start: 0.7817 (t0) cc_final: 0.7555 (t0) REVERT: C 542 ASP cc_start: 0.8754 (m-30) cc_final: 0.8461 (m-30) REVERT: C 585 TYR cc_start: 0.6959 (t80) cc_final: 0.6377 (t80) REVERT: C 588 TYR cc_start: 0.8079 (t80) cc_final: 0.7302 (t80) REVERT: C 590 GLN cc_start: 0.6590 (mt0) cc_final: 0.6359 (pt0) REVERT: C 594 GLN cc_start: 0.7021 (tt0) cc_final: 0.6696 (tm-30) REVERT: C 614 GLU cc_start: 0.7668 (tt0) cc_final: 0.7272 (tp30) REVERT: D 309 GLU cc_start: 0.8077 (tp30) cc_final: 0.7541 (pt0) REVERT: D 310 LYS cc_start: 0.7223 (mtmt) cc_final: 0.6908 (pttt) REVERT: D 341 ASN cc_start: 0.7952 (p0) cc_final: 0.7643 (p0) REVERT: D 418 ASP cc_start: 0.8404 (t0) cc_final: 0.8149 (m-30) REVERT: D 429 ASP cc_start: 0.8364 (p0) cc_final: 0.8097 (p0) REVERT: D 460 GLU cc_start: 0.8155 (tt0) cc_final: 0.7894 (tt0) REVERT: D 483 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8586 (mt-10) REVERT: D 556 GLU cc_start: 0.8683 (tt0) cc_final: 0.8459 (tt0) REVERT: D 590 GLN cc_start: 0.6977 (mt0) cc_final: 0.6621 (tt0) REVERT: D 594 GLN cc_start: 0.7133 (tt0) cc_final: 0.6775 (tm-30) REVERT: D 597 ASP cc_start: 0.8234 (m-30) cc_final: 0.8013 (m-30) REVERT: D 611 VAL cc_start: 0.8069 (p) cc_final: 0.7853 (p) REVERT: E 248 TYR cc_start: 0.7447 (m-80) cc_final: 0.7241 (m-80) REVERT: E 294 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8134 (mt-10) REVERT: E 309 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7121 (pt0) REVERT: E 310 LYS cc_start: 0.7244 (mtmt) cc_final: 0.6888 (ptmt) REVERT: E 388 MET cc_start: 0.8444 (ttm) cc_final: 0.8185 (ttm) REVERT: E 542 ASP cc_start: 0.8609 (m-30) cc_final: 0.8363 (m-30) REVERT: E 590 GLN cc_start: 0.7033 (mt0) cc_final: 0.6672 (pt0) REVERT: E 594 GLN cc_start: 0.6913 (tt0) cc_final: 0.6358 (tm-30) REVERT: F 309 GLU cc_start: 0.7903 (tp30) cc_final: 0.7102 (pt0) REVERT: F 310 LYS cc_start: 0.7403 (mtmt) cc_final: 0.7048 (pttt) REVERT: F 413 SER cc_start: 0.8260 (t) cc_final: 0.7877 (p) REVERT: F 532 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: F 542 ASP cc_start: 0.8787 (m-30) cc_final: 0.8520 (m-30) REVERT: F 594 GLN cc_start: 0.7101 (tt0) cc_final: 0.6760 (tm-30) REVERT: G 341 ASN cc_start: 0.8032 (p0) cc_final: 0.7697 (p0) REVERT: G 419 ILE cc_start: 0.8769 (mt) cc_final: 0.8523 (mt) REVERT: G 429 ASP cc_start: 0.8622 (p0) cc_final: 0.8260 (p0) REVERT: G 483 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8335 (mt-10) REVERT: G 487 GLU cc_start: 0.8455 (pt0) cc_final: 0.8189 (pt0) REVERT: G 542 ASP cc_start: 0.8835 (m-30) cc_final: 0.8633 (m-30) REVERT: G 589 ARG cc_start: 0.6219 (ttt-90) cc_final: 0.5881 (ttt-90) REVERT: G 590 GLN cc_start: 0.6735 (mt0) cc_final: 0.6288 (pt0) REVERT: G 594 GLN cc_start: 0.7141 (tt0) cc_final: 0.6734 (tm-30) REVERT: G 611 VAL cc_start: 0.8288 (p) cc_final: 0.8018 (p) REVERT: H 248 TYR cc_start: 0.7533 (m-80) cc_final: 0.7285 (m-80) REVERT: H 294 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8025 (mt-10) REVERT: H 309 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7076 (pt0) REVERT: H 341 ASN cc_start: 0.7853 (p0) cc_final: 0.7562 (p0) REVERT: H 373 TYR cc_start: 0.6852 (t80) cc_final: 0.6472 (t80) REVERT: H 395 MET cc_start: 0.8131 (ttp) cc_final: 0.7778 (ttp) REVERT: H 429 ASP cc_start: 0.8575 (p0) cc_final: 0.8309 (p0) REVERT: H 509 GLN cc_start: 0.8534 (pt0) cc_final: 0.8226 (pp30) REVERT: H 585 TYR cc_start: 0.7136 (t80) cc_final: 0.6811 (t80) REVERT: H 590 GLN cc_start: 0.6656 (mt0) cc_final: 0.6309 (pt0) REVERT: H 594 GLN cc_start: 0.7316 (tt0) cc_final: 0.6927 (tm-30) REVERT: I 294 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8128 (mt-10) REVERT: I 309 GLU cc_start: 0.7979 (tp30) cc_final: 0.7331 (pt0) REVERT: I 310 LYS cc_start: 0.7531 (mtmt) cc_final: 0.7206 (pttt) REVERT: I 418 ASP cc_start: 0.8472 (t0) cc_final: 0.8067 (m-30) REVERT: I 460 GLU cc_start: 0.8088 (tt0) cc_final: 0.7820 (tt0) REVERT: I 478 ASP cc_start: 0.8310 (m-30) cc_final: 0.7386 (p0) REVERT: I 483 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8349 (mt-10) REVERT: I 542 ASP cc_start: 0.8629 (m-30) cc_final: 0.8365 (m-30) REVERT: I 588 TYR cc_start: 0.8088 (t80) cc_final: 0.7583 (t80) REVERT: I 590 GLN cc_start: 0.6790 (mt0) cc_final: 0.6523 (pt0) REVERT: J 171 ILE cc_start: 0.3922 (OUTLIER) cc_final: 0.3679 (mp) REVERT: J 257 ASN cc_start: 0.6931 (t0) cc_final: 0.6683 (t0) REVERT: J 294 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8409 (mt-10) REVERT: J 341 ASN cc_start: 0.8205 (p0) cc_final: 0.7892 (p0) REVERT: J 429 ASP cc_start: 0.8527 (p0) cc_final: 0.8232 (p0) REVERT: J 460 GLU cc_start: 0.8180 (tt0) cc_final: 0.7693 (mp0) REVERT: J 483 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8549 (mt-10) REVERT: J 509 GLN cc_start: 0.8512 (pt0) cc_final: 0.8049 (tm-30) REVERT: J 588 TYR cc_start: 0.7858 (t80) cc_final: 0.6936 (t80) REVERT: J 594 GLN cc_start: 0.7174 (tt0) cc_final: 0.6533 (tm-30) REVERT: J 611 VAL cc_start: 0.8043 (p) cc_final: 0.7825 (p) REVERT: K 142 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.3795 (mp) REVERT: K 295 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8409 (mp10) REVERT: K 302 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7976 (p) REVERT: K 429 ASP cc_start: 0.8568 (p0) cc_final: 0.8292 (p0) REVERT: K 460 GLU cc_start: 0.8165 (tt0) cc_final: 0.7952 (tt0) REVERT: K 485 GLU cc_start: 0.8612 (tt0) cc_final: 0.8384 (tt0) REVERT: K 575 ASP cc_start: 0.8402 (m-30) cc_final: 0.8108 (t0) REVERT: K 585 TYR cc_start: 0.7215 (t80) cc_final: 0.6812 (t80) REVERT: K 590 GLN cc_start: 0.7226 (mt0) cc_final: 0.6806 (pt0) REVERT: K 594 GLN cc_start: 0.7147 (tt0) cc_final: 0.6776 (tm-30) REVERT: K 611 VAL cc_start: 0.8233 (p) cc_final: 0.8014 (p) REVERT: L 257 ASN cc_start: 0.7121 (t0) cc_final: 0.6327 (m110) REVERT: L 309 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7392 (pt0) REVERT: L 310 LYS cc_start: 0.7164 (mtmt) cc_final: 0.6923 (pttt) REVERT: L 429 ASP cc_start: 0.8773 (p0) cc_final: 0.8536 (p0) REVERT: L 483 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8427 (mt-10) REVERT: L 486 GLN cc_start: 0.8456 (pt0) cc_final: 0.8133 (pp30) REVERT: L 487 GLU cc_start: 0.8495 (pt0) cc_final: 0.8219 (pt0) REVERT: L 590 GLN cc_start: 0.6773 (mt0) cc_final: 0.6395 (pt0) REVERT: L 594 GLN cc_start: 0.6633 (tt0) cc_final: 0.6377 (tt0) REVERT: M 309 GLU cc_start: 0.7738 (tp30) cc_final: 0.7016 (pt0) REVERT: M 310 LYS cc_start: 0.7488 (mtmt) cc_final: 0.7226 (pttt) REVERT: M 341 ASN cc_start: 0.8202 (p0) cc_final: 0.7728 (p0) REVERT: M 483 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8522 (mt-10) REVERT: M 542 ASP cc_start: 0.8759 (m-30) cc_final: 0.8488 (m-30) REVERT: M 588 TYR cc_start: 0.8121 (t80) cc_final: 0.7783 (t80) REVERT: M 594 GLN cc_start: 0.7044 (tt0) cc_final: 0.6596 (tm-30) REVERT: N 310 LYS cc_start: 0.7079 (mtmt) cc_final: 0.6596 (pttt) REVERT: N 341 ASN cc_start: 0.8035 (p0) cc_final: 0.7780 (p0) REVERT: N 399 PHE cc_start: 0.6296 (m-80) cc_final: 0.5904 (m-80) REVERT: N 483 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8562 (mt-10) REVERT: N 542 ASP cc_start: 0.8755 (m-30) cc_final: 0.8452 (m-30) REVERT: N 560 ARG cc_start: 0.8618 (ttm170) cc_final: 0.8414 (ttp-170) REVERT: N 590 GLN cc_start: 0.6688 (mt0) cc_final: 0.6317 (pt0) REVERT: N 594 GLN cc_start: 0.7183 (tt0) cc_final: 0.6761 (tm-30) REVERT: O 302 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7975 (p) REVERT: O 310 LYS cc_start: 0.7335 (mtmt) cc_final: 0.7112 (pttt) REVERT: O 341 ASN cc_start: 0.7969 (p0) cc_final: 0.7587 (p0) REVERT: O 374 LYS cc_start: 0.7961 (mttt) cc_final: 0.7698 (mptt) REVERT: O 395 MET cc_start: 0.8310 (ttp) cc_final: 0.7990 (ttp) REVERT: O 460 GLU cc_start: 0.8222 (tt0) cc_final: 0.7999 (tt0) REVERT: O 483 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8561 (mt-10) REVERT: O 486 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8187 (pp30) REVERT: O 509 GLN cc_start: 0.8530 (pt0) cc_final: 0.8287 (pp30) REVERT: O 542 ASP cc_start: 0.8865 (m-30) cc_final: 0.8551 (m-30) REVERT: O 560 ARG cc_start: 0.8473 (ttm170) cc_final: 0.8223 (ttp-170) REVERT: O 590 GLN cc_start: 0.6718 (mt0) cc_final: 0.6444 (pt0) REVERT: O 594 GLN cc_start: 0.7023 (tt0) cc_final: 0.6773 (tm-30) REVERT: O 611 VAL cc_start: 0.8228 (p) cc_final: 0.8023 (p) outliers start: 116 outliers final: 48 residues processed: 871 average time/residue: 0.6148 time to fit residues: 909.1826 Evaluate side-chains 645 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 590 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 532 GLU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 395 MET Chi-restraints excluded: chain G residue 546 VAL Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 464 VAL Chi-restraints excluded: chain J residue 486 GLN Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 395 MET Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 171 ILE Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 539 LEU Chi-restraints excluded: chain N residue 546 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 486 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 355 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 532 optimal weight: 4.9990 chunk 435 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 641 optimal weight: 1.9990 chunk 692 optimal weight: 2.9990 chunk 571 optimal weight: 8.9990 chunk 636 optimal weight: 0.5980 chunk 218 optimal weight: 0.9980 chunk 514 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 308 GLN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 436 ASN ** E 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 436 ASN ** H 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 257 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 486 GLN J 590 GLN ** K 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 GLN M 308 GLN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 486 GLN ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 257 ASN O 475 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 55095 Z= 0.279 Angle : 0.644 12.201 74745 Z= 0.342 Chirality : 0.048 0.187 9090 Planarity : 0.005 0.045 9690 Dihedral : 5.867 56.847 7552 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.08 % Favored : 97.70 % Rotamer: Outliers : 2.02 % Allowed : 10.27 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.95 (0.09), residues: 6960 helix: -0.06 (0.11), residues: 1875 sheet: -0.50 (0.09), residues: 3015 loop : -1.03 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 404 HIS 0.002 0.001 HIS N 135 PHE 0.016 0.002 PHE O 529 TYR 0.029 0.002 TYR M 577 ARG 0.006 0.001 ARG M 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 635 time to evaluate : 5.811 Fit side-chains REVERT: A 294 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 295 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8434 (mm-40) REVERT: A 310 LYS cc_start: 0.7474 (mtmt) cc_final: 0.7114 (pttt) REVERT: A 341 ASN cc_start: 0.8403 (p0) cc_final: 0.8133 (p0) REVERT: A 373 TYR cc_start: 0.6745 (t80) cc_final: 0.6435 (t80) REVERT: A 374 LYS cc_start: 0.7870 (mttt) cc_final: 0.7658 (mptt) REVERT: A 542 ASP cc_start: 0.8639 (m-30) cc_final: 0.8346 (m-30) REVERT: A 575 ASP cc_start: 0.8461 (m-30) cc_final: 0.8136 (t0) REVERT: A 588 TYR cc_start: 0.8230 (t80) cc_final: 0.7672 (t80) REVERT: A 594 GLN cc_start: 0.7358 (tt0) cc_final: 0.7117 (tt0) REVERT: B 257 ASN cc_start: 0.6936 (t0) cc_final: 0.6677 (t0) REVERT: B 295 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8455 (mm-40) REVERT: B 305 GLN cc_start: 0.6388 (tm-30) cc_final: 0.5965 (tm-30) REVERT: B 341 ASN cc_start: 0.8168 (p0) cc_final: 0.7646 (p0) REVERT: B 373 TYR cc_start: 0.7105 (t80) cc_final: 0.6668 (t80) REVERT: B 418 ASP cc_start: 0.8334 (t0) cc_final: 0.8036 (m-30) REVERT: B 542 ASP cc_start: 0.8593 (m-30) cc_final: 0.8304 (m-30) REVERT: C 249 TYR cc_start: 0.8973 (m-10) cc_final: 0.8437 (m-10) REVERT: C 295 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8616 (mm-40) REVERT: C 304 ASP cc_start: 0.6111 (p0) cc_final: 0.5804 (p0) REVERT: C 310 LYS cc_start: 0.7364 (mtmt) cc_final: 0.6930 (pttt) REVERT: C 388 MET cc_start: 0.8480 (ttm) cc_final: 0.8239 (ttp) REVERT: C 418 ASP cc_start: 0.8532 (t0) cc_final: 0.8130 (m-30) REVERT: C 429 ASP cc_start: 0.8578 (p0) cc_final: 0.8306 (p0) REVERT: C 460 GLU cc_start: 0.8337 (tt0) cc_final: 0.8070 (tt0) REVERT: C 478 ASP cc_start: 0.8156 (m-30) cc_final: 0.7275 (p0) REVERT: C 542 ASP cc_start: 0.8607 (m-30) cc_final: 0.8279 (m-30) REVERT: C 588 TYR cc_start: 0.8160 (t80) cc_final: 0.7656 (t80) REVERT: C 590 GLN cc_start: 0.6699 (mt0) cc_final: 0.6469 (pt0) REVERT: C 594 GLN cc_start: 0.6985 (tt0) cc_final: 0.6641 (tm-30) REVERT: C 614 GLU cc_start: 0.7620 (tt0) cc_final: 0.7186 (tp30) REVERT: D 125 MET cc_start: 0.0564 (tmm) cc_final: 0.0116 (mpp) REVERT: D 341 ASN cc_start: 0.8144 (p0) cc_final: 0.7811 (p0) REVERT: D 418 ASP cc_start: 0.8407 (t0) cc_final: 0.8189 (m-30) REVERT: D 460 GLU cc_start: 0.8241 (tt0) cc_final: 0.7953 (tt0) REVERT: D 478 ASP cc_start: 0.8128 (m-30) cc_final: 0.7259 (p0) REVERT: D 483 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8666 (mt-10) REVERT: D 556 GLU cc_start: 0.8697 (tt0) cc_final: 0.8473 (tt0) REVERT: D 563 MET cc_start: 0.9190 (mtt) cc_final: 0.8963 (mtt) REVERT: D 590 GLN cc_start: 0.6852 (mt0) cc_final: 0.6507 (tt0) REVERT: D 594 GLN cc_start: 0.7185 (tt0) cc_final: 0.6775 (tm-30) REVERT: D 611 VAL cc_start: 0.8121 (p) cc_final: 0.7905 (p) REVERT: E 171 ILE cc_start: 0.3904 (OUTLIER) cc_final: 0.3650 (tp) REVERT: E 294 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8116 (mt-10) REVERT: E 310 LYS cc_start: 0.7388 (mtmt) cc_final: 0.7043 (pttt) REVERT: E 388 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8300 (ttm) REVERT: E 418 ASP cc_start: 0.8524 (t0) cc_final: 0.8195 (m-30) REVERT: E 542 ASP cc_start: 0.8552 (m-30) cc_final: 0.8325 (m-30) REVERT: E 590 GLN cc_start: 0.7089 (mt0) cc_final: 0.6682 (pt0) REVERT: E 594 GLN cc_start: 0.6982 (tt0) cc_final: 0.6407 (tm-30) REVERT: F 249 TYR cc_start: 0.8983 (m-10) cc_final: 0.8427 (m-10) REVERT: F 310 LYS cc_start: 0.7532 (mtmt) cc_final: 0.7179 (pttt) REVERT: F 328 GLU cc_start: 0.8995 (mp0) cc_final: 0.8777 (mt-10) REVERT: F 542 ASP cc_start: 0.8721 (m-30) cc_final: 0.8440 (m-30) REVERT: F 594 GLN cc_start: 0.7071 (tt0) cc_final: 0.6742 (tm-30) REVERT: G 249 TYR cc_start: 0.9044 (m-10) cc_final: 0.8547 (m-10) REVERT: G 429 ASP cc_start: 0.8785 (p0) cc_final: 0.8446 (p0) REVERT: G 483 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8384 (mt-10) REVERT: G 486 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8241 (pp30) REVERT: G 487 GLU cc_start: 0.8577 (pt0) cc_final: 0.8366 (pt0) REVERT: G 542 ASP cc_start: 0.8788 (m-30) cc_final: 0.8466 (m-30) REVERT: G 589 ARG cc_start: 0.6386 (ttt-90) cc_final: 0.6035 (ttt-90) REVERT: G 590 GLN cc_start: 0.6794 (mt0) cc_final: 0.6324 (tt0) REVERT: G 594 GLN cc_start: 0.7212 (tt0) cc_final: 0.6821 (tm-30) REVERT: G 611 VAL cc_start: 0.8360 (p) cc_final: 0.8033 (p) REVERT: H 248 TYR cc_start: 0.7435 (m-80) cc_final: 0.7004 (m-80) REVERT: H 294 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8108 (mt-10) REVERT: H 361 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8659 (pp) REVERT: H 395 MET cc_start: 0.8083 (ttp) cc_final: 0.7811 (ttp) REVERT: H 478 ASP cc_start: 0.8008 (m-30) cc_final: 0.7341 (p0) REVERT: H 509 GLN cc_start: 0.8422 (pt0) cc_final: 0.8221 (pp30) REVERT: H 590 GLN cc_start: 0.6662 (mt0) cc_final: 0.6286 (pt0) REVERT: I 171 ILE cc_start: 0.4360 (OUTLIER) cc_final: 0.3933 (tp) REVERT: I 294 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8144 (mt-10) REVERT: I 295 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8581 (mp10) REVERT: I 310 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7278 (pttt) REVERT: I 373 TYR cc_start: 0.6810 (t80) cc_final: 0.6355 (t80) REVERT: I 460 GLU cc_start: 0.8101 (tt0) cc_final: 0.7900 (tt0) REVERT: I 478 ASP cc_start: 0.7941 (m-30) cc_final: 0.7123 (p0) REVERT: I 483 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8265 (mt-10) REVERT: I 542 ASP cc_start: 0.8572 (m-30) cc_final: 0.8291 (m-30) REVERT: I 574 ASP cc_start: 0.7034 (t0) cc_final: 0.6818 (t0) REVERT: I 588 TYR cc_start: 0.8183 (t80) cc_final: 0.7809 (t80) REVERT: I 590 GLN cc_start: 0.6836 (mt0) cc_final: 0.6493 (pt0) REVERT: J 460 GLU cc_start: 0.8171 (tt0) cc_final: 0.7613 (mp0) REVERT: J 483 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8482 (mt-10) REVERT: J 594 GLN cc_start: 0.7145 (tt0) cc_final: 0.6511 (tm-30) REVERT: J 611 VAL cc_start: 0.8183 (p) cc_final: 0.7942 (p) REVERT: K 295 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8554 (mp10) REVERT: K 429 ASP cc_start: 0.8689 (p0) cc_final: 0.8480 (p0) REVERT: K 485 GLU cc_start: 0.8662 (tt0) cc_final: 0.8428 (tt0) REVERT: K 575 ASP cc_start: 0.8277 (m-30) cc_final: 0.7966 (t0) REVERT: K 590 GLN cc_start: 0.7439 (mt0) cc_final: 0.7087 (pt0) REVERT: K 594 GLN cc_start: 0.7206 (tt0) cc_final: 0.6756 (tm-30) REVERT: L 259 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7836 (t) REVERT: L 310 LYS cc_start: 0.7476 (mtmt) cc_final: 0.7182 (pttt) REVERT: L 374 LYS cc_start: 0.8113 (mttt) cc_final: 0.7880 (mptt) REVERT: L 429 ASP cc_start: 0.8740 (p0) cc_final: 0.8460 (p0) REVERT: L 483 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8470 (mt-10) REVERT: L 487 GLU cc_start: 0.8468 (pt0) cc_final: 0.8077 (pt0) REVERT: L 594 GLN cc_start: 0.6940 (tt0) cc_final: 0.6622 (tt0) REVERT: M 310 LYS cc_start: 0.7620 (mtmt) cc_final: 0.7291 (pttt) REVERT: M 341 ASN cc_start: 0.8416 (p0) cc_final: 0.8048 (p0) REVERT: M 483 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8496 (mt-10) REVERT: M 542 ASP cc_start: 0.8709 (m-30) cc_final: 0.8232 (m-30) REVERT: M 594 GLN cc_start: 0.6996 (tt0) cc_final: 0.6483 (tm-30) REVERT: N 310 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6762 (pttt) REVERT: N 483 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8508 (mt-10) REVERT: N 533 GLN cc_start: 0.8015 (tt0) cc_final: 0.7665 (tm-30) REVERT: N 542 ASP cc_start: 0.8728 (m-30) cc_final: 0.8408 (m-30) REVERT: N 560 ARG cc_start: 0.8664 (ttm170) cc_final: 0.8407 (ttp-170) REVERT: N 590 GLN cc_start: 0.6765 (mt0) cc_final: 0.6413 (pt0) REVERT: N 594 GLN cc_start: 0.7251 (tt0) cc_final: 0.6741 (tm-30) REVERT: O 302 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7951 (p) REVERT: O 310 LYS cc_start: 0.7533 (mtmt) cc_final: 0.7169 (pttt) REVERT: O 395 MET cc_start: 0.8258 (ttp) cc_final: 0.7960 (ttp) REVERT: O 460 GLU cc_start: 0.8232 (tt0) cc_final: 0.7997 (tt0) REVERT: O 483 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8588 (mt-10) REVERT: O 486 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8291 (pp30) REVERT: O 509 GLN cc_start: 0.8614 (pt0) cc_final: 0.8351 (pp30) REVERT: O 590 GLN cc_start: 0.6783 (mt0) cc_final: 0.6537 (pt0) REVERT: O 594 GLN cc_start: 0.6930 (tt0) cc_final: 0.6605 (tm-30) REVERT: O 611 VAL cc_start: 0.8295 (p) cc_final: 0.8057 (p) outliers start: 123 outliers final: 56 residues processed: 727 average time/residue: 0.5834 time to fit residues: 738.2480 Evaluate side-chains 634 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 570 time to evaluate : 6.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 563 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 395 MET Chi-restraints excluded: chain G residue 415 ASN Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 486 GLN Chi-restraints excluded: chain G residue 533 GLN Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 546 VAL Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 464 VAL Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain K residue 395 MET Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 546 VAL Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 444 LEU Chi-restraints excluded: chain O residue 486 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 633 optimal weight: 1.9990 chunk 482 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 306 optimal weight: 8.9990 chunk 430 optimal weight: 10.0000 chunk 643 optimal weight: 1.9990 chunk 681 optimal weight: 3.9990 chunk 336 optimal weight: 9.9990 chunk 610 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN C 475 ASN D 335 GLN D 475 ASN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 ASN F 295 GLN F 335 GLN G 473 GLN G 475 ASN ** H 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 GLN H 475 ASN I 475 ASN J 335 GLN J 475 ASN K 475 ASN L 335 GLN L 475 ASN L 590 GLN M 335 GLN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 335 GLN ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 308 GLN O 335 GLN O 473 GLN O 475 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 55095 Z= 0.400 Angle : 0.671 11.317 74745 Z= 0.353 Chirality : 0.049 0.199 9090 Planarity : 0.005 0.049 9690 Dihedral : 5.800 58.932 7552 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.70 % Favored : 97.28 % Rotamer: Outliers : 3.03 % Allowed : 12.41 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.71 (0.10), residues: 6960 helix: 0.43 (0.12), residues: 1920 sheet: -0.56 (0.09), residues: 2985 loop : -0.88 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 386 HIS 0.002 0.001 HIS B 173 PHE 0.019 0.002 PHE O 529 TYR 0.029 0.002 TYR O 577 ARG 0.007 0.001 ARG C 506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 582 time to evaluate : 6.382 Fit side-chains REVERT: A 294 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8382 (mt-10) REVERT: A 295 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8280 (mm-40) REVERT: A 310 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7303 (pttt) REVERT: A 342 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8489 (pt) REVERT: A 374 LYS cc_start: 0.7914 (mttt) cc_final: 0.7628 (mptt) REVERT: A 418 ASP cc_start: 0.8473 (t0) cc_final: 0.8010 (m-30) REVERT: A 533 GLN cc_start: 0.8235 (tt0) cc_final: 0.7780 (tm-30) REVERT: A 542 ASP cc_start: 0.8852 (m-30) cc_final: 0.8503 (m-30) REVERT: A 575 ASP cc_start: 0.8323 (m-30) cc_final: 0.8046 (t0) REVERT: A 588 TYR cc_start: 0.8170 (t80) cc_final: 0.7634 (t80) REVERT: A 594 GLN cc_start: 0.7363 (tt0) cc_final: 0.6808 (tm-30) REVERT: B 248 TYR cc_start: 0.7384 (m-80) cc_final: 0.6930 (m-80) REVERT: B 257 ASN cc_start: 0.7141 (t0) cc_final: 0.6778 (t0) REVERT: B 295 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8400 (mm-40) REVERT: B 305 GLN cc_start: 0.6517 (tm-30) cc_final: 0.6016 (tm-30) REVERT: B 341 ASN cc_start: 0.8252 (p0) cc_final: 0.7696 (p0) REVERT: B 373 TYR cc_start: 0.7100 (t80) cc_final: 0.6680 (t80) REVERT: B 418 ASP cc_start: 0.8556 (t0) cc_final: 0.8158 (m-30) REVERT: B 542 ASP cc_start: 0.8548 (m-30) cc_final: 0.8247 (m-30) REVERT: C 295 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8613 (mm-40) REVERT: C 310 LYS cc_start: 0.7377 (mtmt) cc_final: 0.6946 (pttt) REVERT: C 418 ASP cc_start: 0.8631 (t0) cc_final: 0.8220 (m-30) REVERT: C 429 ASP cc_start: 0.8625 (p0) cc_final: 0.8423 (p0) REVERT: C 460 GLU cc_start: 0.8417 (tt0) cc_final: 0.8169 (tt0) REVERT: C 478 ASP cc_start: 0.7967 (m-30) cc_final: 0.7043 (p0) REVERT: C 542 ASP cc_start: 0.8722 (m-30) cc_final: 0.8423 (m-30) REVERT: C 590 GLN cc_start: 0.6791 (mt0) cc_final: 0.6408 (tt0) REVERT: C 594 GLN cc_start: 0.6916 (tt0) cc_final: 0.6522 (tm-30) REVERT: D 125 MET cc_start: 0.0830 (tmm) cc_final: 0.0335 (mpp) REVERT: D 309 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7478 (pt0) REVERT: D 460 GLU cc_start: 0.8243 (tt0) cc_final: 0.7947 (tt0) REVERT: D 483 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8562 (mt-10) REVERT: D 556 GLU cc_start: 0.8635 (tt0) cc_final: 0.8410 (tt0) REVERT: D 594 GLN cc_start: 0.6980 (tt0) cc_final: 0.6627 (tm-30) REVERT: D 611 VAL cc_start: 0.8242 (p) cc_final: 0.8020 (p) REVERT: E 125 MET cc_start: 0.1187 (tmm) cc_final: 0.0340 (mpp) REVERT: E 171 ILE cc_start: 0.4111 (OUTLIER) cc_final: 0.3846 (mt) REVERT: E 294 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 310 LYS cc_start: 0.7414 (mtmt) cc_final: 0.7087 (pttt) REVERT: E 486 GLN cc_start: 0.8676 (pt0) cc_final: 0.8284 (pp30) REVERT: E 542 ASP cc_start: 0.8595 (m-30) cc_final: 0.8326 (m-30) REVERT: E 590 GLN cc_start: 0.6908 (mt0) cc_final: 0.6464 (pt0) REVERT: E 594 GLN cc_start: 0.7107 (tt0) cc_final: 0.6524 (tm-30) REVERT: F 249 TYR cc_start: 0.8951 (m-10) cc_final: 0.8562 (m-10) REVERT: F 257 ASN cc_start: 0.6641 (t0) cc_final: 0.6245 (m110) REVERT: F 310 LYS cc_start: 0.7516 (mtmt) cc_final: 0.7211 (pttt) REVERT: F 542 ASP cc_start: 0.8762 (m-30) cc_final: 0.8469 (m-30) REVERT: F 594 GLN cc_start: 0.6998 (tt0) cc_final: 0.6636 (tm-30) REVERT: G 171 ILE cc_start: 0.4101 (OUTLIER) cc_final: 0.3890 (tp) REVERT: G 342 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8304 (pt) REVERT: G 429 ASP cc_start: 0.8791 (p0) cc_final: 0.8472 (p0) REVERT: G 483 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8454 (mt-10) REVERT: G 487 GLU cc_start: 0.8657 (pt0) cc_final: 0.8391 (pt0) REVERT: G 542 ASP cc_start: 0.8991 (m-30) cc_final: 0.8767 (m-30) REVERT: G 590 GLN cc_start: 0.6817 (mt0) cc_final: 0.6367 (tt0) REVERT: G 594 GLN cc_start: 0.7245 (tt0) cc_final: 0.6717 (tm-30) REVERT: G 611 VAL cc_start: 0.8520 (p) cc_final: 0.8270 (p) REVERT: H 248 TYR cc_start: 0.7456 (m-80) cc_final: 0.7008 (m-80) REVERT: H 294 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8167 (mt-10) REVERT: H 361 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8625 (pp) REVERT: H 373 TYR cc_start: 0.6643 (t80) cc_final: 0.6250 (t80) REVERT: H 395 MET cc_start: 0.8044 (ttp) cc_final: 0.7804 (ttp) REVERT: H 418 ASP cc_start: 0.8487 (t0) cc_final: 0.8234 (m-30) REVERT: H 509 GLN cc_start: 0.8422 (pt0) cc_final: 0.8178 (pp30) REVERT: H 590 GLN cc_start: 0.6669 (mt0) cc_final: 0.6309 (pt0) REVERT: H 594 GLN cc_start: 0.7240 (tt0) cc_final: 0.6865 (tm-30) REVERT: I 310 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7277 (pttt) REVERT: I 373 TYR cc_start: 0.6841 (t80) cc_final: 0.6374 (t80) REVERT: I 418 ASP cc_start: 0.8548 (t0) cc_final: 0.8112 (m-30) REVERT: I 478 ASP cc_start: 0.7802 (m-30) cc_final: 0.7051 (p0) REVERT: I 483 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8357 (mt-10) REVERT: I 486 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8243 (pp30) REVERT: I 542 ASP cc_start: 0.8566 (m-30) cc_final: 0.8265 (m-30) REVERT: I 590 GLN cc_start: 0.6857 (mt0) cc_final: 0.6460 (tt0) REVERT: J 342 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8448 (pp) REVERT: J 460 GLU cc_start: 0.8202 (tt0) cc_final: 0.7644 (mp0) REVERT: J 483 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8510 (mt-10) REVERT: J 532 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: J 590 GLN cc_start: 0.7152 (mt0) cc_final: 0.6758 (pt0) REVERT: J 594 GLN cc_start: 0.7170 (tt0) cc_final: 0.6614 (tm-30) REVERT: J 611 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8086 (p) REVERT: K 485 GLU cc_start: 0.8724 (tt0) cc_final: 0.8494 (tt0) REVERT: K 486 GLN cc_start: 0.8719 (pt0) cc_final: 0.8443 (pp30) REVERT: K 533 GLN cc_start: 0.8420 (tt0) cc_final: 0.8029 (tm-30) REVERT: K 590 GLN cc_start: 0.7194 (mt0) cc_final: 0.6893 (pt0) REVERT: K 594 GLN cc_start: 0.7234 (tt0) cc_final: 0.6701 (tm-30) REVERT: K 607 GLU cc_start: 0.8111 (pm20) cc_final: 0.7878 (pm20) REVERT: L 259 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7873 (t) REVERT: L 310 LYS cc_start: 0.7487 (mtmt) cc_final: 0.7159 (pttt) REVERT: L 374 LYS cc_start: 0.8141 (mttt) cc_final: 0.7897 (mptt) REVERT: L 415 ASN cc_start: 0.8815 (p0) cc_final: 0.8319 (p0) REVERT: L 483 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8446 (mt-10) REVERT: L 487 GLU cc_start: 0.8543 (pt0) cc_final: 0.8172 (pt0) REVERT: L 594 GLN cc_start: 0.6865 (tt0) cc_final: 0.6534 (tt0) REVERT: M 310 LYS cc_start: 0.7612 (mtmt) cc_final: 0.7325 (pttt) REVERT: M 483 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8558 (mt-10) REVERT: M 542 ASP cc_start: 0.8910 (m-30) cc_final: 0.8564 (m-30) REVERT: M 594 GLN cc_start: 0.6963 (tt0) cc_final: 0.6410 (tm-30) REVERT: N 309 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7668 (pt0) REVERT: N 310 LYS cc_start: 0.7202 (mtmt) cc_final: 0.6731 (pttt) REVERT: N 373 TYR cc_start: 0.7061 (t80) cc_final: 0.6444 (t80) REVERT: N 429 ASP cc_start: 0.8758 (p0) cc_final: 0.8535 (p0) REVERT: N 483 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8528 (mt-10) REVERT: N 542 ASP cc_start: 0.8741 (m-30) cc_final: 0.8454 (m-30) REVERT: N 560 ARG cc_start: 0.8725 (ttm170) cc_final: 0.8471 (ttp-170) REVERT: N 594 GLN cc_start: 0.7284 (tt0) cc_final: 0.6640 (tm-30) REVERT: O 295 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8440 (mp10) REVERT: O 302 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7980 (p) REVERT: O 310 LYS cc_start: 0.7477 (mtmt) cc_final: 0.7115 (pttt) REVERT: O 395 MET cc_start: 0.8272 (ttp) cc_final: 0.7973 (ttp) REVERT: O 460 GLU cc_start: 0.8278 (tt0) cc_final: 0.8019 (tt0) REVERT: O 483 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8648 (mt-10) REVERT: O 486 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8331 (pp30) REVERT: O 509 GLN cc_start: 0.8547 (pt0) cc_final: 0.8301 (pp30) REVERT: O 590 GLN cc_start: 0.6848 (mt0) cc_final: 0.6240 (pt0) REVERT: O 594 GLN cc_start: 0.7141 (tt0) cc_final: 0.6701 (tm-30) REVERT: O 611 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8112 (p) outliers start: 184 outliers final: 106 residues processed: 720 average time/residue: 0.5998 time to fit residues: 755.8579 Evaluate side-chains 672 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 553 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 415 ASN Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 475 ASN Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 563 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 415 ASN Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 395 MET Chi-restraints excluded: chain G residue 415 ASN Chi-restraints excluded: chain G residue 458 THR Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 533 GLN Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 546 VAL Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 534 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 486 GLN Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 539 LEU Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 415 ASN Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 464 VAL Chi-restraints excluded: chain J residue 484 ILE Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 534 VAL Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain J residue 611 VAL Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain K residue 395 MET Chi-restraints excluded: chain K residue 458 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 534 VAL Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain L residue 458 THR Chi-restraints excluded: chain L residue 459 VAL Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 458 THR Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 539 LEU Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 498 THR Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 539 LEU Chi-restraints excluded: chain N residue 546 VAL Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 291 THR Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 342 LEU Chi-restraints excluded: chain O residue 419 ILE Chi-restraints excluded: chain O residue 444 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain O residue 459 VAL Chi-restraints excluded: chain O residue 486 GLN Chi-restraints excluded: chain O residue 498 THR Chi-restraints excluded: chain O residue 534 VAL Chi-restraints excluded: chain O residue 611 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 567 optimal weight: 0.1980 chunk 386 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 507 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 581 optimal weight: 3.9990 chunk 471 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 347 optimal weight: 0.9980 chunk 611 optimal weight: 30.0000 chunk 171 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 GLN E 475 ASN F 257 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 GLN ** H 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 257 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 GLN ** L 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 295 GLN ** M 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 GLN ** O 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 55095 Z= 0.216 Angle : 0.583 11.164 74745 Z= 0.306 Chirality : 0.046 0.168 9090 Planarity : 0.005 0.045 9690 Dihedral : 5.358 57.282 7552 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.34 % Allowed : 14.67 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.41 (0.10), residues: 6960 helix: 0.83 (0.12), residues: 1950 sheet: -0.54 (0.09), residues: 3015 loop : -0.63 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 346 HIS 0.002 0.000 HIS I 173 PHE 0.014 0.001 PHE C 529 TYR 0.017 0.002 TYR K 373 ARG 0.007 0.000 ARG K 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13920 Ramachandran restraints generated. 6960 Oldfield, 0 Emsley, 6960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 607 time to evaluate : 5.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8419 (mt-10) REVERT: A 295 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8339 (mm-40) REVERT: A 310 LYS cc_start: 0.7493 (mtmt) cc_final: 0.7130 (pttt) REVERT: A 373 TYR cc_start: 0.6650 (t80) cc_final: 0.6405 (t80) REVERT: A 374 LYS cc_start: 0.7898 (mttt) cc_final: 0.7645 (mptt) REVERT: A 418 ASP cc_start: 0.8339 (t0) cc_final: 0.7889 (m-30) REVERT: A 533 GLN cc_start: 0.8096 (tt0) cc_final: 0.7701 (tm-30) REVERT: A 542 ASP cc_start: 0.8623 (m-30) cc_final: 0.8333 (m-30) REVERT: A 575 ASP cc_start: 0.8371 (m-30) cc_final: 0.8104 (t0) REVERT: A 588 TYR cc_start: 0.8060 (t80) cc_final: 0.7539 (t80) REVERT: A 594 GLN cc_start: 0.7296 (tt0) cc_final: 0.6726 (tm-30) REVERT: B 248 TYR cc_start: 0.7445 (m-80) cc_final: 0.6933 (m-80) REVERT: B 295 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8535 (mm-40) REVERT: B 305 GLN cc_start: 0.6483 (tm-30) cc_final: 0.5920 (tm-30) REVERT: B 341 ASN cc_start: 0.8120 (p0) cc_final: 0.7737 (p0) REVERT: B 373 TYR cc_start: 0.7017 (t80) cc_final: 0.6586 (t80) REVERT: B 418 ASP cc_start: 0.8465 (t0) cc_final: 0.8088 (m-30) REVERT: B 434 SER cc_start: 0.8986 (p) cc_final: 0.8746 (t) REVERT: B 542 ASP cc_start: 0.8476 (m-30) cc_final: 0.8160 (m-30) REVERT: C 249 TYR cc_start: 0.8804 (m-10) cc_final: 0.8328 (m-10) REVERT: C 295 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8561 (mm-40) REVERT: C 310 LYS cc_start: 0.7347 (mtmt) cc_final: 0.6931 (pttt) REVERT: C 388 MET cc_start: 0.8493 (ttm) cc_final: 0.8258 (ttp) REVERT: C 418 ASP cc_start: 0.8536 (t0) cc_final: 0.8167 (m-30) REVERT: C 429 ASP cc_start: 0.8597 (p0) cc_final: 0.8388 (p0) REVERT: C 460 GLU cc_start: 0.8409 (tt0) cc_final: 0.8127 (tt0) REVERT: C 478 ASP cc_start: 0.8044 (m-30) cc_final: 0.7215 (p0) REVERT: C 533 GLN cc_start: 0.8371 (tt0) cc_final: 0.7987 (tm-30) REVERT: C 542 ASP cc_start: 0.8659 (m-30) cc_final: 0.8297 (m-30) REVERT: C 590 GLN cc_start: 0.6753 (mt0) cc_final: 0.6351 (tt0) REVERT: C 594 GLN cc_start: 0.6909 (tt0) cc_final: 0.6465 (tm-30) REVERT: C 597 ASP cc_start: 0.7896 (m-30) cc_final: 0.7593 (m-30) REVERT: D 125 MET cc_start: 0.1236 (tmm) cc_final: 0.0601 (mpp) REVERT: D 309 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7396 (pt0) REVERT: D 418 ASP cc_start: 0.8394 (t0) cc_final: 0.8114 (m-30) REVERT: D 460 GLU cc_start: 0.8263 (tt0) cc_final: 0.7970 (tt0) REVERT: D 478 ASP cc_start: 0.8074 (m-30) cc_final: 0.7284 (p0) REVERT: D 483 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8558 (mt-10) REVERT: D 556 GLU cc_start: 0.8603 (tt0) cc_final: 0.8365 (tt0) REVERT: D 594 GLN cc_start: 0.6981 (tt0) cc_final: 0.6543 (tm-30) REVERT: D 611 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.8020 (p) REVERT: E 125 MET cc_start: 0.1188 (tmm) cc_final: 0.0354 (mpp) REVERT: E 293 ASP cc_start: 0.8172 (t0) cc_final: 0.7965 (t70) REVERT: E 294 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7958 (mt-10) REVERT: E 310 LYS cc_start: 0.7327 (mtmt) cc_final: 0.6936 (ptmt) REVERT: E 341 ASN cc_start: 0.8233 (p0) cc_final: 0.7657 (p0) REVERT: E 418 ASP cc_start: 0.8483 (t0) cc_final: 0.8105 (m-30) REVERT: E 478 ASP cc_start: 0.7859 (m-30) cc_final: 0.7238 (p0) REVERT: E 486 GLN cc_start: 0.8597 (pt0) cc_final: 0.8241 (pp30) REVERT: E 513 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9095 (tp) REVERT: E 542 ASP cc_start: 0.8445 (m-30) cc_final: 0.8180 (m-30) REVERT: E 590 GLN cc_start: 0.6875 (mt0) cc_final: 0.6366 (pt0) REVERT: E 594 GLN cc_start: 0.7353 (tt0) cc_final: 0.6782 (tm-30) REVERT: F 249 TYR cc_start: 0.8795 (m-10) cc_final: 0.8339 (m-10) REVERT: F 310 LYS cc_start: 0.7455 (mtmt) cc_final: 0.7176 (pttt) REVERT: F 542 ASP cc_start: 0.8680 (m-30) cc_final: 0.8397 (m-30) REVERT: F 594 GLN cc_start: 0.6924 (tt0) cc_final: 0.6602 (tm-30) REVERT: G 249 TYR cc_start: 0.8933 (m-10) cc_final: 0.8462 (m-10) REVERT: G 341 ASN cc_start: 0.8311 (p0) cc_final: 0.7677 (p0) REVERT: G 429 ASP cc_start: 0.8782 (p0) cc_final: 0.8467 (p0) REVERT: G 483 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8388 (mt-10) REVERT: G 487 GLU cc_start: 0.8735 (pt0) cc_final: 0.8310 (pt0) REVERT: G 542 ASP cc_start: 0.8833 (m-30) cc_final: 0.8557 (m-30) REVERT: G 590 GLN cc_start: 0.6779 (mt0) cc_final: 0.6281 (tt0) REVERT: G 594 GLN cc_start: 0.7175 (tt0) cc_final: 0.6633 (tm-30) REVERT: H 248 TYR cc_start: 0.7435 (m-80) cc_final: 0.7031 (m-80) REVERT: H 294 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8062 (mt-10) REVERT: H 373 TYR cc_start: 0.6646 (t80) cc_final: 0.6247 (t80) REVERT: H 395 MET cc_start: 0.8023 (ttp) cc_final: 0.7777 (ttp) REVERT: H 417 ASN cc_start: 0.8213 (t0) cc_final: 0.8002 (t0) REVERT: H 478 ASP cc_start: 0.7735 (m-30) cc_final: 0.7144 (p0) REVERT: H 509 GLN cc_start: 0.8449 (pt0) cc_final: 0.8222 (pp30) REVERT: H 590 GLN cc_start: 0.6680 (mt0) cc_final: 0.6281 (pt0) REVERT: I 294 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8042 (mt-10) REVERT: I 310 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7252 (pttt) REVERT: I 373 TYR cc_start: 0.6795 (t80) cc_final: 0.6367 (t80) REVERT: I 390 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8789 (m) REVERT: I 418 ASP cc_start: 0.8434 (t0) cc_final: 0.8197 (m-30) REVERT: I 478 ASP cc_start: 0.7883 (m-30) cc_final: 0.7160 (p0) REVERT: I 483 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8314 (mt-10) REVERT: I 542 ASP cc_start: 0.8545 (m-30) cc_final: 0.8266 (m-30) REVERT: I 590 GLN cc_start: 0.6797 (mt0) cc_final: 0.6357 (tt0) REVERT: I 611 VAL cc_start: 0.8082 (p) cc_final: 0.7882 (p) REVERT: J 417 ASN cc_start: 0.8159 (t0) cc_final: 0.7871 (t0) REVERT: J 460 GLU cc_start: 0.8177 (tt0) cc_final: 0.7659 (mp0) REVERT: J 483 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8467 (mt-10) REVERT: J 532 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: J 533 GLN cc_start: 0.8245 (tt0) cc_final: 0.7939 (tm-30) REVERT: J 594 GLN cc_start: 0.7157 (tt0) cc_final: 0.6603 (tm-30) REVERT: K 295 GLN cc_start: 0.8871 (mm110) cc_final: 0.8477 (mp10) REVERT: K 485 GLU cc_start: 0.8664 (tt0) cc_final: 0.8432 (tt0) REVERT: K 486 GLN cc_start: 0.8676 (pt0) cc_final: 0.8431 (pp30) REVERT: K 533 GLN cc_start: 0.8346 (tt0) cc_final: 0.7967 (tm-30) REVERT: K 590 GLN cc_start: 0.7443 (mt0) cc_final: 0.7085 (pt0) REVERT: K 594 GLN cc_start: 0.7194 (tt0) cc_final: 0.6614 (tm-30) REVERT: L 259 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7925 (t) REVERT: L 310 LYS cc_start: 0.7436 (mtmt) cc_final: 0.7125 (pttt) REVERT: L 341 ASN cc_start: 0.8185 (p0) cc_final: 0.7751 (p0) REVERT: L 374 LYS cc_start: 0.8148 (mttt) cc_final: 0.7926 (mptt) REVERT: L 415 ASN cc_start: 0.8700 (p0) cc_final: 0.8228 (p0) REVERT: L 418 ASP cc_start: 0.8453 (t0) cc_final: 0.8006 (m-30) REVERT: L 483 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8409 (mt-10) REVERT: L 487 GLU cc_start: 0.8560 (pt0) cc_final: 0.8211 (pt0) REVERT: L 594 GLN cc_start: 0.6811 (tt0) cc_final: 0.6503 (tt0) REVERT: M 310 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7306 (pttt) REVERT: M 341 ASN cc_start: 0.8272 (p0) cc_final: 0.7861 (p0) REVERT: M 483 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8477 (mt-10) REVERT: M 486 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8372 (pp30) REVERT: M 542 ASP cc_start: 0.8798 (m-30) cc_final: 0.8309 (m-30) REVERT: M 594 GLN cc_start: 0.6930 (tt0) cc_final: 0.6378 (tm-30) REVERT: N 309 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7545 (pt0) REVERT: N 310 LYS cc_start: 0.7150 (mtmt) cc_final: 0.6682 (pttt) REVERT: N 373 TYR cc_start: 0.7054 (t80) cc_final: 0.6829 (t80) REVERT: N 399 PHE cc_start: 0.6394 (m-80) cc_final: 0.6041 (m-80) REVERT: N 483 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8546 (mt-10) REVERT: N 542 ASP cc_start: 0.8655 (m-30) cc_final: 0.8314 (m-30) REVERT: N 560 ARG cc_start: 0.8676 (ttm170) cc_final: 0.8412 (ttp-170) REVERT: N 590 GLN cc_start: 0.6906 (mt0) cc_final: 0.6522 (pt0) REVERT: N 594 GLN cc_start: 0.7263 (tt0) cc_final: 0.6625 (tm-30) REVERT: O 295 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8334 (mp10) REVERT: O 302 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7994 (p) REVERT: O 310 LYS cc_start: 0.7429 (mtmt) cc_final: 0.7072 (pttt) REVERT: O 395 MET cc_start: 0.8225 (ttp) cc_final: 0.7921 (ttp) REVERT: O 460 GLU cc_start: 0.8275 (tt0) cc_final: 0.8030 (tt0) REVERT: O 483 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8582 (mt-10) REVERT: O 486 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8313 (pp30) REVERT: O 509 GLN cc_start: 0.8556 (pt0) cc_final: 0.8297 (pp30) REVERT: O 590 GLN cc_start: 0.6831 (mt0) cc_final: 0.6231 (tt0) REVERT: O 594 GLN cc_start: 0.7125 (tt0) cc_final: 0.6673 (tm-30) REVERT: O 611 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8155 (p) outliers start: 142 outliers final: 89 residues processed: 717 average time/residue: 0.5903 time to fit residues: 740.8217 Evaluate side-chains 665 residues out of total 6075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 567 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 336 ASP Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 563 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 486 GLN Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 546 VAL Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 458 THR Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 415 ASN Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain I residue 459 VAL Chi-restraints excluded: chain I residue 484 ILE Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 413 SER Chi-restraints excluded: chain J residue 458 THR Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 534 VAL Chi-restraints excluded: chain J residue 546 VAL Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 336 ASP Chi-restraints excluded: chain K residue 458 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 534 VAL Chi-restraints excluded: chain K residue 546 VAL Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain L residue 291 THR Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 458 THR Chi-restraints excluded: chain L residue 459 VAL Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain M residue 258 LEU Chi-restraints excluded: chain M residue 458 THR Chi-restraints excluded: chain M residue 486 GLN Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 546 VAL Chi-restraints excluded: chain N residue 142 LEU Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 534 VAL Chi-restraints excluded: chain N residue 546 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 291 THR Chi-restraints excluded: chain O residue 302 THR Chi-restraints excluded: chain O residue 332 VAL Chi-restraints excluded: chain O residue 419 ILE Chi-restraints excluded: chain O residue 444 LEU Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain O residue 486 GLN Chi-restraints excluded: chain O residue 534 VAL Chi-restraints excluded: chain O residue 611 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 229 optimal weight: 1.9990 chunk 613 optimal weight: 5.9990 chunk 134 optimal weight: 0.0020 chunk 400 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 682 optimal weight: 5.9990 chunk 566 optimal weight: 2.9990 chunk 315 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 358 optimal weight: 0.6980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: