Starting phenix.real_space_refine on Wed Nov 20 07:27:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/11_2024/8pe8_17629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/11_2024/8pe8_17629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/11_2024/8pe8_17629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/11_2024/8pe8_17629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/11_2024/8pe8_17629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/11_2024/8pe8_17629.cif" } resolution = 3.46 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= 0.009 sd= 0.116 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 168 5.16 5 C 34300 2.51 5 N 9450 2.21 5 O 10864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54782 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3913 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 14, 'TRANS': 513} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, N Time building chain proxies: 13.82, per 1000 atoms: 0.25 Number of scatterers: 54782 At special positions: 0 Unit cell: (164.16, 164.16, 168, 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 168 16.00 O 10864 8.00 N 9450 7.00 C 34300 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: 13.68 Conformation dependent library (CDL) restraints added in 6.9 seconds 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13412 Finding SS restraints... Secondary structure from input PDB file: 266 helices and 84 sheets defined 56.2% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.34 Creating SS restraints... Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 90 through 111 Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 138 through 161 Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 259 through 270 removed outlier: 3.576A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 307 through 322 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 436 Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.986A pdb=" N GLN A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 528 through 546 Processing helix chain 'B' and resid 35 through 55 removed outlier: 3.782A pdb=" N THR B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 90 through 111 Processing helix chain 'B' and resid 114 through 135 Processing helix chain 'B' and resid 138 through 161 Processing helix chain 'B' and resid 166 through 178 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.577A pdb=" N LEU B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 307 through 322 Processing helix chain 'B' and resid 364 through 379 Processing helix chain 'B' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 436 Processing helix chain 'B' and resid 443 through 453 Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.986A pdb=" N GLN B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 500 removed outlier: 3.700A pdb=" N VAL B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 523 Processing helix chain 'B' and resid 528 through 546 Processing helix chain 'C' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 90 through 111 Processing helix chain 'C' and resid 114 through 135 Processing helix chain 'C' and resid 138 through 161 Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 259 through 270 removed outlier: 3.576A pdb=" N LEU C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 307 through 322 Processing helix chain 'C' and resid 364 through 379 Processing helix chain 'C' and resid 385 through 401 removed outlier: 4.009A pdb=" N GLY C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 436 Processing helix chain 'C' and resid 443 through 453 Processing helix chain 'C' and resid 461 through 476 removed outlier: 3.986A pdb=" N GLN C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR C 476 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA C 486 " --> pdb=" O ILE C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 523 Processing helix chain 'C' and resid 528 through 546 Processing helix chain 'D' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 85 Processing helix chain 'D' and resid 90 through 111 Processing helix chain 'D' and resid 114 through 135 Processing helix chain 'D' and resid 138 through 161 Processing helix chain 'D' and resid 166 through 178 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 259 through 270 removed outlier: 3.576A pdb=" N LEU D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 307 through 322 Processing helix chain 'D' and resid 364 through 379 Processing helix chain 'D' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 436 Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.987A pdb=" N GLN D 465 " --> pdb=" O ASN D 461 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 487 removed outlier: 3.669A pdb=" N ALA D 486 " --> pdb=" O ILE D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL D 493 " --> pdb=" O GLU D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 523 Processing helix chain 'D' and resid 528 through 546 Processing helix chain 'E' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'E' and resid 90 through 111 Processing helix chain 'E' and resid 114 through 135 Processing helix chain 'E' and resid 138 through 161 Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 259 through 270 removed outlier: 3.577A pdb=" N LEU E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 307 through 322 Processing helix chain 'E' and resid 364 through 379 Processing helix chain 'E' and resid 385 through 401 removed outlier: 4.009A pdb=" N GLY E 401 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 436 Processing helix chain 'E' and resid 443 through 453 Processing helix chain 'E' and resid 461 through 476 removed outlier: 3.987A pdb=" N GLN E 465 " --> pdb=" O ASN E 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR E 476 " --> pdb=" O LYS E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA E 486 " --> pdb=" O ILE E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 500 removed outlier: 3.700A pdb=" N VAL E 493 " --> pdb=" O GLU E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 523 Processing helix chain 'E' and resid 528 through 546 Processing helix chain 'F' and resid 35 through 55 removed outlier: 3.784A pdb=" N THR F 55 " --> pdb=" O LYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'F' and resid 90 through 111 Processing helix chain 'F' and resid 114 through 135 Processing helix chain 'F' and resid 138 through 161 Processing helix chain 'F' and resid 166 through 178 Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 259 through 270 removed outlier: 3.576A pdb=" N LEU F 263 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 292 Processing helix chain 'F' and resid 307 through 322 Processing helix chain 'F' and resid 364 through 379 Processing helix chain 'F' and resid 385 through 401 removed outlier: 4.009A pdb=" N GLY F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 436 Processing helix chain 'F' and resid 443 through 453 Processing helix chain 'F' and resid 461 through 476 removed outlier: 3.987A pdb=" N GLN F 465 " --> pdb=" O ASN F 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR F 476 " --> pdb=" O LYS F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA F 486 " --> pdb=" O ILE F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL F 493 " --> pdb=" O GLU F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 Processing helix chain 'F' and resid 528 through 546 Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'G' and resid 90 through 111 Processing helix chain 'G' and resid 114 through 135 Processing helix chain 'G' and resid 138 through 161 Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 182 through 196 Processing helix chain 'G' and resid 259 through 270 removed outlier: 3.577A pdb=" N LEU G 263 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 292 Processing helix chain 'G' and resid 307 through 322 Processing helix chain 'G' and resid 364 through 379 Processing helix chain 'G' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY G 401 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 436 Processing helix chain 'G' and resid 443 through 453 Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.987A pdb=" N GLN G 465 " --> pdb=" O ASN G 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR G 476 " --> pdb=" O LYS G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA G 486 " --> pdb=" O ILE G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL G 493 " --> pdb=" O GLU G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 523 Processing helix chain 'G' and resid 528 through 546 Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 85 Processing helix chain 'H' and resid 90 through 111 Processing helix chain 'H' and resid 114 through 135 Processing helix chain 'H' and resid 138 through 161 Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 182 through 196 Processing helix chain 'H' and resid 259 through 270 removed outlier: 3.576A pdb=" N LEU H 263 " --> pdb=" O ILE H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 292 Processing helix chain 'H' and resid 307 through 322 Processing helix chain 'H' and resid 364 through 379 Processing helix chain 'H' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 436 Processing helix chain 'H' and resid 443 through 453 Processing helix chain 'H' and resid 461 through 476 removed outlier: 3.986A pdb=" N GLN H 465 " --> pdb=" O ASN H 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR H 476 " --> pdb=" O LYS H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA H 486 " --> pdb=" O ILE H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL H 493 " --> pdb=" O GLU H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 523 Processing helix chain 'H' and resid 528 through 546 Processing helix chain 'I' and resid 35 through 55 removed outlier: 3.782A pdb=" N THR I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 85 Processing helix chain 'I' and resid 90 through 111 Processing helix chain 'I' and resid 114 through 135 Processing helix chain 'I' and resid 138 through 161 Processing helix chain 'I' and resid 166 through 178 Processing helix chain 'I' and resid 182 through 196 Processing helix chain 'I' and resid 259 through 270 removed outlier: 3.577A pdb=" N LEU I 263 " --> pdb=" O ILE I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 292 Processing helix chain 'I' and resid 307 through 322 Processing helix chain 'I' and resid 364 through 379 Processing helix chain 'I' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY I 401 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 436 Processing helix chain 'I' and resid 443 through 453 Processing helix chain 'I' and resid 461 through 476 removed outlier: 3.986A pdb=" N GLN I 465 " --> pdb=" O ASN I 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR I 476 " --> pdb=" O LYS I 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA I 486 " --> pdb=" O ILE I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 489 through 500 removed outlier: 3.700A pdb=" N VAL I 493 " --> pdb=" O GLU I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 518 through 523 Processing helix chain 'I' and resid 528 through 546 Processing helix chain 'J' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR J 55 " --> pdb=" O LYS J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 85 Processing helix chain 'J' and resid 90 through 111 Processing helix chain 'J' and resid 114 through 135 Processing helix chain 'J' and resid 138 through 161 Processing helix chain 'J' and resid 166 through 178 Processing helix chain 'J' and resid 182 through 196 Processing helix chain 'J' and resid 259 through 270 removed outlier: 3.576A pdb=" N LEU J 263 " --> pdb=" O ILE J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 292 Processing helix chain 'J' and resid 307 through 322 Processing helix chain 'J' and resid 364 through 379 Processing helix chain 'J' and resid 385 through 401 removed outlier: 4.009A pdb=" N GLY J 401 " --> pdb=" O ALA J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 412 through 436 Processing helix chain 'J' and resid 443 through 453 Processing helix chain 'J' and resid 461 through 476 removed outlier: 3.986A pdb=" N GLN J 465 " --> pdb=" O ASN J 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR J 476 " --> pdb=" O LYS J 472 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA J 486 " --> pdb=" O ILE J 482 " (cutoff:3.500A) Processing helix chain 'J' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL J 493 " --> pdb=" O GLU J 489 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 523 Processing helix chain 'J' and resid 528 through 546 Processing helix chain 'K' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR K 55 " --> pdb=" O LYS K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 85 Processing helix chain 'K' and resid 90 through 111 Processing helix chain 'K' and resid 114 through 135 Processing helix chain 'K' and resid 138 through 161 Processing helix chain 'K' and resid 166 through 178 Processing helix chain 'K' and resid 182 through 196 Processing helix chain 'K' and resid 259 through 270 removed outlier: 3.576A pdb=" N LEU K 263 " --> pdb=" O ILE K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 292 Processing helix chain 'K' and resid 307 through 322 Processing helix chain 'K' and resid 364 through 379 Processing helix chain 'K' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY K 401 " --> pdb=" O ALA K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 436 Processing helix chain 'K' and resid 443 through 453 Processing helix chain 'K' and resid 461 through 476 removed outlier: 3.987A pdb=" N GLN K 465 " --> pdb=" O ASN K 461 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR K 476 " --> pdb=" O LYS K 472 " (cutoff:3.500A) Processing helix chain 'K' and resid 476 through 487 removed outlier: 3.669A pdb=" N ALA K 486 " --> pdb=" O ILE K 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL K 493 " --> pdb=" O GLU K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 518 through 523 Processing helix chain 'K' and resid 528 through 546 Processing helix chain 'L' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR L 55 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 85 Processing helix chain 'L' and resid 90 through 111 Processing helix chain 'L' and resid 114 through 135 Processing helix chain 'L' and resid 138 through 161 Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 196 Processing helix chain 'L' and resid 259 through 270 removed outlier: 3.577A pdb=" N LEU L 263 " --> pdb=" O ILE L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 292 Processing helix chain 'L' and resid 307 through 322 Processing helix chain 'L' and resid 364 through 379 Processing helix chain 'L' and resid 385 through 401 removed outlier: 4.009A pdb=" N GLY L 401 " --> pdb=" O ALA L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 436 Processing helix chain 'L' and resid 443 through 453 Processing helix chain 'L' and resid 461 through 476 removed outlier: 3.987A pdb=" N GLN L 465 " --> pdb=" O ASN L 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR L 476 " --> pdb=" O LYS L 472 " (cutoff:3.500A) Processing helix chain 'L' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA L 486 " --> pdb=" O ILE L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 500 removed outlier: 3.700A pdb=" N VAL L 493 " --> pdb=" O GLU L 489 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 Processing helix chain 'L' and resid 528 through 546 Processing helix chain 'M' and resid 35 through 55 removed outlier: 3.784A pdb=" N THR M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 85 Processing helix chain 'M' and resid 90 through 111 Processing helix chain 'M' and resid 114 through 135 Processing helix chain 'M' and resid 138 through 161 Processing helix chain 'M' and resid 166 through 178 Processing helix chain 'M' and resid 182 through 196 Processing helix chain 'M' and resid 259 through 270 removed outlier: 3.576A pdb=" N LEU M 263 " --> pdb=" O ILE M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 292 Processing helix chain 'M' and resid 307 through 322 Processing helix chain 'M' and resid 364 through 379 Processing helix chain 'M' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY M 401 " --> pdb=" O ALA M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 436 Processing helix chain 'M' and resid 443 through 453 Processing helix chain 'M' and resid 461 through 476 removed outlier: 3.987A pdb=" N GLN M 465 " --> pdb=" O ASN M 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR M 476 " --> pdb=" O LYS M 472 " (cutoff:3.500A) Processing helix chain 'M' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA M 486 " --> pdb=" O ILE M 482 " (cutoff:3.500A) Processing helix chain 'M' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL M 493 " --> pdb=" O GLU M 489 " (cutoff:3.500A) Processing helix chain 'M' and resid 518 through 523 Processing helix chain 'M' and resid 528 through 546 Processing helix chain 'N' and resid 35 through 55 removed outlier: 3.783A pdb=" N THR N 55 " --> pdb=" O LYS N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 85 Processing helix chain 'N' and resid 90 through 111 Processing helix chain 'N' and resid 114 through 135 Processing helix chain 'N' and resid 138 through 161 Processing helix chain 'N' and resid 166 through 178 Processing helix chain 'N' and resid 182 through 196 Processing helix chain 'N' and resid 259 through 270 removed outlier: 3.577A pdb=" N LEU N 263 " --> pdb=" O ILE N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 292 Processing helix chain 'N' and resid 307 through 322 Processing helix chain 'N' and resid 364 through 379 Processing helix chain 'N' and resid 385 through 401 removed outlier: 4.008A pdb=" N GLY N 401 " --> pdb=" O ALA N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 436 Processing helix chain 'N' and resid 443 through 453 Processing helix chain 'N' and resid 461 through 476 removed outlier: 3.987A pdb=" N GLN N 465 " --> pdb=" O ASN N 461 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR N 476 " --> pdb=" O LYS N 472 " (cutoff:3.500A) Processing helix chain 'N' and resid 476 through 487 removed outlier: 3.670A pdb=" N ALA N 486 " --> pdb=" O ILE N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 500 removed outlier: 3.699A pdb=" N VAL N 493 " --> pdb=" O GLU N 489 " (cutoff:3.500A) Processing helix chain 'N' and resid 518 through 523 Processing helix chain 'N' and resid 528 through 546 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL A 553 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE A 406 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 202 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 216 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 405 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU A 359 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 348 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 361 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 346 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 344 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE A 275 " --> pdb=" O VAL A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 439 Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL B 553 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA9, first strand: chain 'B' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE B 406 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 202 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 216 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 405 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU B 359 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 348 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY B 361 " --> pdb=" O THR B 346 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 346 " --> pdb=" O GLY B 361 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 344 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE B 275 " --> pdb=" O VAL B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AB4, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL C 553 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE C 406 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR C 202 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 216 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 405 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU C 359 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 348 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY C 361 " --> pdb=" O THR C 346 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C 346 " --> pdb=" O GLY C 361 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 344 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE C 275 " --> pdb=" O VAL C 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 438 through 439 Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL D 553 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC3, first strand: chain 'D' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE D 406 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR D 202 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 216 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 405 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 218 through 221 removed outlier: 3.514A pdb=" N LEU D 359 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY D 361 " --> pdb=" O THR D 346 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR D 346 " --> pdb=" O GLY D 361 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 344 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE D 275 " --> pdb=" O VAL D 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 438 through 439 Processing sheet with id=AC7, first strand: chain 'E' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL E 553 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AC9, first strand: chain 'E' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE E 406 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR E 202 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 216 " --> pdb=" O VAL E 403 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E 405 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU E 359 " --> pdb=" O SER E 348 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER E 348 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY E 361 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR E 346 " --> pdb=" O GLY E 361 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 344 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE E 275 " --> pdb=" O VAL E 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 438 through 439 Processing sheet with id=AD4, first strand: chain 'F' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL F 553 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AD6, first strand: chain 'F' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE F 406 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR F 202 " --> pdb=" O ILE F 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR F 216 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 405 " --> pdb=" O GLU F 214 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 218 through 221 removed outlier: 3.512A pdb=" N LEU F 359 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER F 348 " --> pdb=" O LEU F 359 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY F 361 " --> pdb=" O THR F 346 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR F 346 " --> pdb=" O GLY F 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY F 344 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE F 275 " --> pdb=" O VAL F 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 438 through 439 Processing sheet with id=AE1, first strand: chain 'G' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL G 553 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AE3, first strand: chain 'G' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE G 406 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR G 202 " --> pdb=" O ILE G 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR G 216 " --> pdb=" O VAL G 403 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL G 405 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU G 359 " --> pdb=" O SER G 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER G 348 " --> pdb=" O LEU G 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY G 361 " --> pdb=" O THR G 346 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR G 346 " --> pdb=" O GLY G 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G 344 " --> pdb=" O ILE G 246 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 275 through 276 removed outlier: 6.382A pdb=" N ILE G 275 " --> pdb=" O VAL G 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'G' and resid 438 through 439 Processing sheet with id=AE7, first strand: chain 'H' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL H 553 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 64 through 66 Processing sheet with id=AE9, first strand: chain 'H' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE H 406 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR H 202 " --> pdb=" O ILE H 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR H 216 " --> pdb=" O VAL H 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL H 405 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU H 359 " --> pdb=" O SER H 348 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER H 348 " --> pdb=" O LEU H 359 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY H 361 " --> pdb=" O THR H 346 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR H 346 " --> pdb=" O GLY H 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY H 344 " --> pdb=" O ILE H 246 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE H 275 " --> pdb=" O VAL H 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'H' and resid 438 through 439 Processing sheet with id=AF4, first strand: chain 'I' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL I 553 " --> pdb=" O GLU I 31 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 64 through 66 Processing sheet with id=AF6, first strand: chain 'I' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE I 406 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 202 " --> pdb=" O ILE I 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR I 216 " --> pdb=" O VAL I 403 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL I 405 " --> pdb=" O GLU I 214 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 218 through 221 removed outlier: 3.512A pdb=" N LEU I 359 " --> pdb=" O SER I 348 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER I 348 " --> pdb=" O LEU I 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY I 361 " --> pdb=" O THR I 346 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR I 346 " --> pdb=" O GLY I 361 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY I 344 " --> pdb=" O ILE I 246 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE I 275 " --> pdb=" O VAL I 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'I' and resid 438 through 439 Processing sheet with id=AG1, first strand: chain 'J' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL J 553 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 64 through 66 Processing sheet with id=AG3, first strand: chain 'J' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE J 406 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR J 202 " --> pdb=" O ILE J 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR J 216 " --> pdb=" O VAL J 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL J 405 " --> pdb=" O GLU J 214 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU J 359 " --> pdb=" O SER J 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER J 348 " --> pdb=" O LEU J 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY J 361 " --> pdb=" O THR J 346 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR J 346 " --> pdb=" O GLY J 361 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY J 344 " --> pdb=" O ILE J 246 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE J 275 " --> pdb=" O VAL J 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'J' and resid 438 through 439 Processing sheet with id=AG7, first strand: chain 'K' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL K 553 " --> pdb=" O GLU K 31 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 64 through 66 Processing sheet with id=AG9, first strand: chain 'K' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE K 406 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR K 202 " --> pdb=" O ILE K 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR K 216 " --> pdb=" O VAL K 403 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL K 405 " --> pdb=" O GLU K 214 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 218 through 221 removed outlier: 3.514A pdb=" N LEU K 359 " --> pdb=" O SER K 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER K 348 " --> pdb=" O LEU K 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY K 361 " --> pdb=" O THR K 346 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR K 346 " --> pdb=" O GLY K 361 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY K 344 " --> pdb=" O ILE K 246 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE K 275 " --> pdb=" O VAL K 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'K' and resid 438 through 439 Processing sheet with id=AH4, first strand: chain 'L' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL L 553 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 64 through 66 Processing sheet with id=AH6, first strand: chain 'L' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE L 406 " --> pdb=" O VAL L 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR L 202 " --> pdb=" O ILE L 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR L 216 " --> pdb=" O VAL L 403 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL L 405 " --> pdb=" O GLU L 214 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU L 359 " --> pdb=" O SER L 348 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER L 348 " --> pdb=" O LEU L 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY L 361 " --> pdb=" O THR L 346 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR L 346 " --> pdb=" O GLY L 361 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY L 344 " --> pdb=" O ILE L 246 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE L 275 " --> pdb=" O VAL L 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'L' and resid 438 through 439 Processing sheet with id=AI1, first strand: chain 'M' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL M 553 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 64 through 66 Processing sheet with id=AI3, first strand: chain 'M' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE M 406 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR M 202 " --> pdb=" O ILE M 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR M 216 " --> pdb=" O VAL M 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL M 405 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.512A pdb=" N LEU M 359 " --> pdb=" O SER M 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER M 348 " --> pdb=" O LEU M 359 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY M 361 " --> pdb=" O THR M 346 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR M 346 " --> pdb=" O GLY M 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY M 344 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 275 through 276 removed outlier: 6.383A pdb=" N ILE M 275 " --> pdb=" O VAL M 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'M' and resid 438 through 439 Processing sheet with id=AI7, first strand: chain 'N' and resid 31 through 34 removed outlier: 3.513A pdb=" N VAL N 553 " --> pdb=" O GLU N 31 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 64 through 66 Processing sheet with id=AI9, first strand: chain 'N' and resid 200 through 202 removed outlier: 3.684A pdb=" N ILE N 406 " --> pdb=" O VAL N 200 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR N 202 " --> pdb=" O ILE N 406 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR N 216 " --> pdb=" O VAL N 403 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL N 405 " --> pdb=" O GLU N 214 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 218 through 221 removed outlier: 3.513A pdb=" N LEU N 359 " --> pdb=" O SER N 348 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER N 348 " --> pdb=" O LEU N 359 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY N 361 " --> pdb=" O THR N 346 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR N 346 " --> pdb=" O GLY N 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY N 344 " --> pdb=" O ILE N 246 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 275 through 276 removed outlier: 6.382A pdb=" N ILE N 275 " --> pdb=" O VAL N 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'N' and resid 438 through 439 3262 hydrogen bonds defined for protein. 9492 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: 23.97 Time building geometry restraints manager: 15.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 18774 1.34 - 1.46: 9233 1.46 - 1.58: 26971 1.58 - 1.69: 0 1.69 - 1.81: 294 Bond restraints: 55272 Sorted by residual: bond pdb=" N GLY D 180 " pdb=" CA GLY D 180 " ideal model delta sigma weight residual 1.449 1.466 -0.017 1.45e-02 4.76e+03 1.30e+00 bond pdb=" N GLY K 180 " pdb=" CA GLY K 180 " ideal model delta sigma weight residual 1.449 1.466 -0.017 1.45e-02 4.76e+03 1.30e+00 bond pdb=" N GLY C 180 " pdb=" CA GLY C 180 " ideal model delta sigma weight residual 1.449 1.465 -0.016 1.45e-02 4.76e+03 1.25e+00 bond pdb=" N GLY J 180 " pdb=" CA GLY J 180 " ideal model delta sigma weight residual 1.449 1.465 -0.016 1.45e-02 4.76e+03 1.25e+00 bond pdb=" N GLY B 180 " pdb=" CA GLY B 180 " ideal model delta sigma weight residual 1.449 1.465 -0.016 1.45e-02 4.76e+03 1.25e+00 ... (remaining 55267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 71673 1.15 - 2.30: 2229 2.30 - 3.45: 482 3.45 - 4.59: 166 4.59 - 5.74: 70 Bond angle restraints: 74620 Sorted by residual: angle pdb=" C VAL I 424 " pdb=" N ASP I 425 " pdb=" CA ASP I 425 " ideal model delta sigma weight residual 120.29 116.86 3.43 1.42e+00 4.96e-01 5.82e+00 angle pdb=" C VAL B 424 " pdb=" N ASP B 425 " pdb=" CA ASP B 425 " ideal model delta sigma weight residual 120.29 116.86 3.43 1.42e+00 4.96e-01 5.82e+00 angle pdb=" C VAL A 424 " pdb=" N ASP A 425 " pdb=" CA ASP A 425 " ideal model delta sigma weight residual 120.29 116.87 3.42 1.42e+00 4.96e-01 5.78e+00 angle pdb=" C VAL H 424 " pdb=" N ASP H 425 " pdb=" CA ASP H 425 " ideal model delta sigma weight residual 120.29 116.87 3.42 1.42e+00 4.96e-01 5.78e+00 angle pdb=" C VAL F 424 " pdb=" N ASP F 425 " pdb=" CA ASP F 425 " ideal model delta sigma weight residual 120.29 116.88 3.41 1.42e+00 4.96e-01 5.76e+00 ... (remaining 74615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 28420 17.93 - 35.86: 4298 35.86 - 53.79: 1078 53.79 - 71.72: 236 71.72 - 89.65: 72 Dihedral angle restraints: 34104 sinusoidal: 13244 harmonic: 20860 Sorted by residual: dihedral pdb=" CA ASP J 281 " pdb=" CB ASP J 281 " pdb=" CG ASP J 281 " pdb=" OD1 ASP J 281 " ideal model delta sinusoidal sigma weight residual -30.00 -87.88 57.88 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP C 281 " pdb=" CB ASP C 281 " pdb=" CG ASP C 281 " pdb=" OD1 ASP C 281 " ideal model delta sinusoidal sigma weight residual -30.00 -87.88 57.88 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP I 281 " pdb=" CB ASP I 281 " pdb=" CG ASP I 281 " pdb=" OD1 ASP I 281 " ideal model delta sinusoidal sigma weight residual -30.00 -87.88 57.88 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 34101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5861 0.030 - 0.060: 2008 0.060 - 0.090: 745 0.090 - 0.120: 416 0.120 - 0.150: 56 Chirality restraints: 9086 Sorted by residual: chirality pdb=" CG LEU E 43 " pdb=" CB LEU E 43 " pdb=" CD1 LEU E 43 " pdb=" CD2 LEU E 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CG LEU L 43 " pdb=" CB LEU L 43 " pdb=" CD1 LEU L 43 " pdb=" CD2 LEU L 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CG LEU N 43 " pdb=" CB LEU N 43 " pdb=" CD1 LEU N 43 " pdb=" CD2 LEU N 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 9083 not shown) Planarity restraints: 9702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP M 421 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" CG ASP M 421 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP M 421 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP M 421 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 421 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" CG ASP F 421 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP F 421 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 421 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 421 " -0.006 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" CG ASP E 421 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP E 421 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP E 421 " -0.008 2.00e-02 2.50e+03 ... (remaining 9699 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 12660 2.79 - 3.32: 55537 3.32 - 3.84: 92776 3.84 - 4.37: 96705 4.37 - 4.90: 174593 Nonbonded interactions: 432271 Sorted by model distance: nonbonded pdb=" OG1 THR D 346 " pdb=" O LEU D 359 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR K 346 " pdb=" O LEU K 359 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR F 346 " pdb=" O LEU F 359 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR M 346 " pdb=" O LEU M 359 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR E 346 " pdb=" O LEU E 359 " model vdw 2.259 3.040 ... (remaining 432266 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' } 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: 1.320 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: 0.050 Extract box with map and model: 2.060 Check model and map are aligned: 0.350 Set scattering table: 0.480 Process input model: 99.130 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.200 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.002 0.031 55272 Z= 0.140 Angle : 0.528 5.743 74620 Z= 0.283 Chirality : 0.040 0.150 9086 Planarity : 0.003 0.029 9702 Dihedral : 18.530 89.651 20692 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.48 % Allowed : 41.38 % Favored : 58.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 7364 helix: 1.84 (0.08), residues: 3962 sheet: -0.91 (0.21), residues: 602 loop : -1.36 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 183 PHE 0.004 0.001 PHE J 225 TYR 0.002 0.000 TYR M 156 ARG 0.006 0.000 ARG J 431 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 765 time to evaluate : 5.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8398 (mt) cc_final: 0.8178 (mt) REVERT: A 170 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7621 (mt) REVERT: A 431 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7764 (mmt180) REVERT: B 89 LYS cc_start: 0.8243 (tppt) cc_final: 0.7868 (tttt) REVERT: B 138 ASN cc_start: 0.8611 (t0) cc_final: 0.8240 (t0) REVERT: B 170 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7711 (mt) REVERT: B 337 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7967 (mtmt) REVERT: B 407 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8761 (mmmm) REVERT: B 431 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7708 (mmt180) REVERT: C 163 ASP cc_start: 0.7278 (t0) cc_final: 0.6998 (t0) REVERT: C 170 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7579 (mt) REVERT: C 431 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7483 (mmt180) REVERT: C 537 ASP cc_start: 0.8479 (m-30) cc_final: 0.7847 (m-30) REVERT: D 170 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7490 (mt) REVERT: D 431 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7791 (mmt180) REVERT: E 144 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7405 (ttm-80) REVERT: E 337 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8104 (mtpp) REVERT: E 431 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7880 (mmt180) REVERT: F 89 LYS cc_start: 0.8367 (tppt) cc_final: 0.8113 (tttt) REVERT: F 170 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7455 (mt) REVERT: F 192 MET cc_start: 0.8830 (ppp) cc_final: 0.8361 (ppp) REVERT: F 242 GLU cc_start: 0.7705 (mp0) cc_final: 0.7489 (mm-30) REVERT: F 303 LYS cc_start: 0.6814 (tttt) cc_final: 0.6558 (tttm) REVERT: F 330 GLU cc_start: 0.6538 (mp0) cc_final: 0.6282 (tm-30) REVERT: F 431 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.7639 (tpp-160) REVERT: G 102 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7785 (tm-30) REVERT: G 106 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7632 (ptmm) REVERT: G 170 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7507 (mt) REVERT: G 271 ARG cc_start: 0.6497 (mpt180) cc_final: 0.6241 (mmt90) REVERT: G 337 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8037 (mtmt) REVERT: H 100 LEU cc_start: 0.8417 (mt) cc_final: 0.8146 (mt) REVERT: H 170 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7633 (mt) REVERT: H 431 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7775 (mmt180) REVERT: I 170 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7686 (mt) REVERT: I 271 ARG cc_start: 0.6844 (mpt180) cc_final: 0.6564 (mmt90) REVERT: I 431 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7874 (tpp-160) REVERT: J 102 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7993 (mt-10) REVERT: J 170 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7479 (mt) REVERT: J 431 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7382 (mmt180) REVERT: J 537 ASP cc_start: 0.8468 (m-30) cc_final: 0.7872 (m-30) REVERT: K 170 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7543 (mt) REVERT: K 431 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.7780 (mmt180) REVERT: L 144 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7396 (ttm-80) REVERT: L 337 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7757 (mtmt) REVERT: L 431 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7832 (mmt180) REVERT: M 89 LYS cc_start: 0.8358 (tppt) cc_final: 0.8042 (tttt) REVERT: M 144 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7353 (ttm-80) REVERT: M 170 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7595 (mt) REVERT: M 192 MET cc_start: 0.8893 (ppp) cc_final: 0.8413 (ppp) REVERT: M 330 GLU cc_start: 0.6639 (mp0) cc_final: 0.6415 (tm-30) REVERT: M 431 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7637 (mmt180) REVERT: N 89 LYS cc_start: 0.8273 (tppt) cc_final: 0.8068 (tttp) REVERT: N 102 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7625 (tm-30) REVERT: N 106 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7781 (mtmt) REVERT: N 170 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7348 (mt) REVERT: N 337 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8132 (mtmt) REVERT: N 537 ASP cc_start: 0.8146 (m-30) cc_final: 0.7482 (m-30) outliers start: 28 outliers final: 3 residues processed: 789 average time/residue: 0.6387 time to fit residues: 843.0006 Evaluate side-chains 650 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 635 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 326 VAL Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain N residue 170 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 3.9990 chunk 551 optimal weight: 0.6980 chunk 306 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 570 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 chunk 424 optimal weight: 6.9990 chunk 661 optimal weight: 30.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 464 GLN B 132 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN C 29 HIS C 132 ASN C 464 GLN D 132 ASN D 464 GLN E 29 HIS E 132 ASN E 464 GLN F 132 ASN F 464 GLN G 29 HIS G 132 ASN G 464 GLN H 29 HIS H 132 ASN H 464 GLN I 132 ASN ** I 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 GLN J 132 ASN J 464 GLN K 132 ASN K 464 GLN L 29 HIS L 132 ASN L 464 GLN M 132 ASN M 172 GLN M 464 GLN ** N 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 ASN N 464 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 55272 Z= 0.250 Angle : 0.553 7.228 74620 Z= 0.290 Chirality : 0.042 0.163 9086 Planarity : 0.004 0.100 9702 Dihedral : 3.870 41.741 7755 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.13 % Allowed : 37.20 % Favored : 58.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 7364 helix: 1.88 (0.08), residues: 3976 sheet: -1.15 (0.19), residues: 770 loop : -1.33 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 29 PHE 0.025 0.002 PHE K 221 TYR 0.004 0.001 TYR N 501 ARG 0.006 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 630 time to evaluate : 5.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8220 (mt-10) REVERT: A 170 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7919 (mt) REVERT: A 312 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8522 (pttt) REVERT: A 431 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7794 (mmt180) REVERT: B 89 LYS cc_start: 0.8532 (tppt) cc_final: 0.7987 (tttt) REVERT: B 138 ASN cc_start: 0.8755 (t0) cc_final: 0.8399 (t0) REVERT: B 170 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7962 (mt) REVERT: B 337 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8067 (mtmt) REVERT: B 407 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8754 (mmmm) REVERT: B 431 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7865 (tpp-160) REVERT: C 88 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8727 (mm) REVERT: C 163 ASP cc_start: 0.7017 (t0) cc_final: 0.6782 (p0) REVERT: C 170 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7818 (mt) REVERT: C 192 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8197 (ppp) REVERT: C 431 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7611 (mmt180) REVERT: C 537 ASP cc_start: 0.8507 (m-30) cc_final: 0.7855 (m-30) REVERT: D 170 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7771 (mt) REVERT: D 431 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7817 (mmt180) REVERT: E 144 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7738 (ttp-170) REVERT: E 172 GLN cc_start: 0.8491 (tt0) cc_final: 0.8114 (tp-100) REVERT: E 192 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7656 (ppp) REVERT: E 337 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8075 (mtpp) REVERT: E 431 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.8025 (mpt180) REVERT: F 89 LYS cc_start: 0.8485 (tppt) cc_final: 0.8144 (tttt) REVERT: F 138 ASN cc_start: 0.8675 (t0) cc_final: 0.8187 (t0) REVERT: F 170 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7865 (mt) REVERT: F 192 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8514 (ppp) REVERT: F 330 GLU cc_start: 0.6531 (mp0) cc_final: 0.6247 (tm-30) REVERT: F 387 TYR cc_start: 0.2359 (OUTLIER) cc_final: 0.2004 (m-80) REVERT: F 431 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.8055 (tpp80) REVERT: G 102 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7754 (tm-30) REVERT: G 192 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7797 (ppp) REVERT: G 337 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8076 (mtmt) REVERT: G 431 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.7766 (mmt180) REVERT: G 537 ASP cc_start: 0.8209 (m-30) cc_final: 0.7571 (m-30) REVERT: H 155 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8188 (mm-30) REVERT: H 170 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8006 (mt) REVERT: H 192 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8250 (ppp) REVERT: H 431 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.7761 (tpp-160) REVERT: I 89 LYS cc_start: 0.8639 (tppt) cc_final: 0.7951 (ttmt) REVERT: I 170 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7919 (mt) REVERT: I 431 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7932 (tpp-160) REVERT: J 88 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8728 (mm) REVERT: J 170 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7739 (mt) REVERT: J 192 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8162 (ppp) REVERT: J 431 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7522 (mmt180) REVERT: J 537 ASP cc_start: 0.8493 (m-30) cc_final: 0.7871 (m-30) REVERT: K 170 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7901 (mt) REVERT: K 192 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8114 (ppp) REVERT: K 431 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.7805 (mmt180) REVERT: L 144 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7657 (ttm-80) REVERT: L 163 ASP cc_start: 0.7031 (t0) cc_final: 0.6805 (t0) REVERT: L 192 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.7950 (ppp) REVERT: L 337 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7731 (mtmt) REVERT: L 431 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8038 (mpt180) REVERT: M 89 LYS cc_start: 0.8504 (tppt) cc_final: 0.8062 (tttt) REVERT: M 144 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7687 (ttp-170) REVERT: M 170 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7988 (mt) REVERT: M 192 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8493 (ppp) REVERT: M 330 GLU cc_start: 0.6647 (mp0) cc_final: 0.6396 (tm-30) REVERT: M 387 TYR cc_start: 0.2290 (OUTLIER) cc_final: 0.1896 (m-80) REVERT: M 431 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8053 (tpp80) REVERT: N 102 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7626 (tm-30) REVERT: N 170 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7783 (mt) REVERT: N 337 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7980 (mtmt) REVERT: N 420 LYS cc_start: 0.8297 (tttm) cc_final: 0.7644 (tptm) REVERT: N 537 ASP cc_start: 0.8232 (m-30) cc_final: 0.7564 (m-30) outliers start: 241 outliers final: 147 residues processed: 820 average time/residue: 0.6336 time to fit residues: 885.9006 Evaluate side-chains 754 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 583 time to evaluate : 6.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 470 ILE Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 327 PHE Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 470 ILE Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 326 VAL Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 427 LEU Chi-restraints excluded: chain J residue 470 ILE Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain K residue 470 ILE Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 470 ILE Chi-restraints excluded: chain L residue 492 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 192 MET Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 470 ILE Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 170 ILE Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 427 LEU Chi-restraints excluded: chain N residue 470 ILE Chi-restraints excluded: chain N residue 492 VAL Chi-restraints excluded: chain N residue 530 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 550 optimal weight: 8.9990 chunk 450 optimal weight: 9.9990 chunk 182 optimal weight: 30.0000 chunk 662 optimal weight: 6.9990 chunk 715 optimal weight: 6.9990 chunk 589 optimal weight: 9.9990 chunk 656 optimal weight: 4.9990 chunk 225 optimal weight: 30.0000 chunk 531 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 55272 Z= 0.375 Angle : 0.628 9.107 74620 Z= 0.326 Chirality : 0.044 0.177 9086 Planarity : 0.004 0.069 9702 Dihedral : 4.437 59.961 7750 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 7.98 % Allowed : 33.47 % Favored : 58.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 7364 helix: 1.45 (0.08), residues: 3962 sheet: -1.54 (0.18), residues: 770 loop : -1.24 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 183 PHE 0.032 0.002 PHE L 221 TYR 0.006 0.001 TYR N 501 ARG 0.016 0.001 ARG G 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 466 poor density : 578 time to evaluate : 5.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7050 (pm20) cc_final: 0.6781 (pm20) REVERT: A 102 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8170 (mt-10) REVERT: A 170 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8407 (mt) REVERT: A 312 LYS cc_start: 0.8956 (mmtm) cc_final: 0.8537 (pttt) REVERT: A 420 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7744 (tptm) REVERT: A 431 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7913 (mmt180) REVERT: B 88 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8797 (mm) REVERT: B 89 LYS cc_start: 0.8678 (tppt) cc_final: 0.8151 (ttmt) REVERT: B 138 ASN cc_start: 0.8903 (t0) cc_final: 0.8521 (t0) REVERT: B 170 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8395 (mt) REVERT: B 278 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.4550 (mm-30) REVERT: B 337 LYS cc_start: 0.8349 (ttmm) cc_final: 0.7875 (mtmt) REVERT: B 407 LYS cc_start: 0.9336 (mmmt) cc_final: 0.8746 (mmmm) REVERT: B 431 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8114 (tpp-160) REVERT: B 484 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8478 (tp30) REVERT: C 170 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (mt) REVERT: C 420 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7722 (tptm) REVERT: C 431 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.7832 (mmt180) REVERT: C 537 ASP cc_start: 0.8404 (m-30) cc_final: 0.7803 (m-30) REVERT: D 31 GLU cc_start: 0.7182 (pm20) cc_final: 0.6929 (pm20) REVERT: D 102 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8057 (mt-10) REVERT: D 161 LYS cc_start: 0.8137 (pptt) cc_final: 0.7803 (pptt) REVERT: D 170 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8356 (mt) REVERT: D 271 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6696 (mmt90) REVERT: D 420 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8018 (ttpt) REVERT: D 431 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.7945 (mmt180) REVERT: E 31 GLU cc_start: 0.6995 (pm20) cc_final: 0.6775 (pm20) REVERT: E 192 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7852 (ppp) REVERT: E 271 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6471 (mmt90) REVERT: E 337 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8142 (mtpp) REVERT: E 420 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7758 (tptm) REVERT: E 431 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.7943 (mmp80) REVERT: F 31 GLU cc_start: 0.6763 (pm20) cc_final: 0.6426 (pm20) REVERT: F 75 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7883 (tp) REVERT: F 88 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8783 (mm) REVERT: F 89 LYS cc_start: 0.8595 (tppt) cc_final: 0.8278 (tttt) REVERT: F 138 ASN cc_start: 0.8834 (t0) cc_final: 0.8461 (t0) REVERT: F 170 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8326 (mt) REVERT: F 192 MET cc_start: 0.8943 (ppp) cc_final: 0.8454 (ppp) REVERT: F 278 GLU cc_start: 0.4783 (OUTLIER) cc_final: 0.4003 (mm-30) REVERT: F 387 TYR cc_start: 0.2422 (OUTLIER) cc_final: 0.1905 (m-80) REVERT: F 431 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8027 (mmm160) REVERT: G 31 GLU cc_start: 0.7134 (pm20) cc_final: 0.6823 (pm20) REVERT: G 138 ASN cc_start: 0.8913 (t0) cc_final: 0.8424 (t0) REVERT: G 170 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8057 (mt) REVERT: G 192 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8042 (ppp) REVERT: G 337 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8025 (mtmt) REVERT: G 420 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7620 (tptm) REVERT: G 537 ASP cc_start: 0.8204 (m-30) ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 420 LYS Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 254 SER Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 420 LYS Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 387 TYR Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 254 SER Chi-restraints excluded: chain H residue 271 ARG Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 349 ILE Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 406 ILE Chi-restraints excluded: chain H residue 411 SER Chi-restraints excluded: chain H residue 420 LYS Chi-restraints excluded: chain H residue 470 ILE Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 259 ILE Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 327 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 470 ILE Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain J residue 470 ILE Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 327 PHE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain K residue 356 THR Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 411 SER Chi-restraints excluded: chain K residue 420 LYS Chi-restraints excluded: chain K residue 469 ASN Chi-restraints excluded: chain K residue 470 ILE Chi-restraints excluded: chain K residue 484 GLU Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 267 HIS Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 327 PHE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 470 ILE Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 492 VAL Chi-restraints excluded: chain L residue 520 ILE Chi-restraints excluded: chain L residue 521 GLN Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 553 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 167 SER Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 254 SER Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 349 ILE Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 470 ILE Chi-restraints excluded: chain M residue 492 VAL Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain M residue 545 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 170 ILE Chi-restraints excluded: chain N residue 254 SER Chi-restraints excluded: chain N residue 278 GLU Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 356 THR Chi-restraints excluded: chain N residue 387 TYR Chi-restraints excluded: chain N residue 411 SER Chi-restraints excluded: chain N residue 420 LYS Chi-restraints excluded: chain N residue 470 ILE Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 488 LEU Chi-restraints excluded: chain N residue 492 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 541 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 30.0000 chunk 497 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 316 optimal weight: 4.9990 chunk 444 optimal weight: 8.9990 chunk 664 optimal weight: 0.9980 chunk 703 optimal weight: 5.9990 chunk 347 optimal weight: 30.0000 chunk 629 optimal weight: 2.9990 chunk 189 optimal weight: 40.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN ** I 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 55272 Z= 0.274 Angle : 0.562 8.123 74620 Z= 0.293 Chirality : 0.043 0.187 9086 Planarity : 0.003 0.057 9702 Dihedral : 4.227 58.348 7750 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.97 % Allowed : 34.74 % Favored : 58.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.09), residues: 7364 helix: 1.53 (0.08), residues: 3976 sheet: -1.64 (0.17), residues: 770 loop : -1.27 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 29 PHE 0.020 0.001 PHE G 221 TYR 0.004 0.001 TYR K 387 ARG 0.005 0.000 ARG K 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 407 poor density : 594 time to evaluate : 6.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7170 (pm20) cc_final: 0.6901 (pm20) REVERT: A 89 LYS cc_start: 0.8797 (tppt) cc_final: 0.8356 (tttt) REVERT: A 170 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 271 ARG cc_start: 0.6334 (mmt90) cc_final: 0.6037 (mmt90) REVERT: A 312 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8642 (ptpt) REVERT: A 342 MET cc_start: 0.5369 (pmm) cc_final: 0.5117 (pmm) REVERT: A 420 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7757 (tptm) REVERT: A 431 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.7971 (tpp-160) REVERT: B 31 GLU cc_start: 0.7184 (pm20) cc_final: 0.6883 (pm20) REVERT: B 75 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8037 (tp) REVERT: B 88 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8736 (mm) REVERT: B 89 LYS cc_start: 0.8632 (tppt) cc_final: 0.8143 (ttpt) REVERT: B 138 ASN cc_start: 0.8904 (t0) cc_final: 0.8528 (t0) REVERT: B 170 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8603 (mt) REVERT: B 337 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7854 (mtmt) REVERT: B 407 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8684 (mmmm) REVERT: B 431 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8056 (tpp-160) REVERT: C 102 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8077 (mt-10) REVERT: C 420 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7730 (tptm) REVERT: C 431 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7858 (mmt180) REVERT: C 537 ASP cc_start: 0.8395 (m-30) cc_final: 0.7786 (m-30) REVERT: D 31 GLU cc_start: 0.7315 (pm20) cc_final: 0.7007 (pm20) REVERT: D 62 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8049 (mtt180) REVERT: D 431 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.7926 (mmt180) REVERT: E 31 GLU cc_start: 0.7131 (pm20) cc_final: 0.6884 (pm20) REVERT: E 192 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.7813 (ppp) REVERT: E 271 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6408 (mmt90) REVERT: E 337 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8070 (mtpp) REVERT: E 420 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7704 (tptm) REVERT: E 431 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.7979 (mmp80) REVERT: F 31 GLU cc_start: 0.6870 (pm20) cc_final: 0.6483 (pm20) REVERT: F 88 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8680 (mm) REVERT: F 89 LYS cc_start: 0.8598 (tppt) cc_final: 0.8323 (tttt) REVERT: F 138 ASN cc_start: 0.8792 (t0) cc_final: 0.8437 (t0) REVERT: F 170 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8366 (mt) REVERT: F 192 MET cc_start: 0.8951 (ppp) cc_final: 0.8480 (ppp) REVERT: F 271 ARG cc_start: 0.6815 (mpt180) cc_final: 0.6354 (mmt90) REVERT: F 326 VAL cc_start: 0.5531 (OUTLIER) cc_final: 0.5112 (m) REVERT: F 387 TYR cc_start: 0.2350 (OUTLIER) cc_final: 0.1804 (m-80) REVERT: F 431 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8057 (mmm160) REVERT: G 31 GLU cc_start: 0.7174 (pm20) cc_final: 0.6820 (pm20) REVERT: G 170 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8062 (mt) REVERT: G 192 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.7992 (ppp) REVERT: G 278 GLU cc_start: 0.5294 (OUTLIER) cc_final: 0.4647 (mm-30) REVERT: G 337 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7867 (mtmt) REVERT: G 537 ASP cc_start: 0.8188 (m-30) cc_final: 0.7544 (m-30) REVERT: H 31 GLU cc_start: 0.7060 (pm20) cc_final: 0.6788 (pm20) REVERT: H 89 LYS cc_start: 0.8801 (tppt) cc_final: 0.8470 (ttpt) REVERT: H 128 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8229 (mm-30) REVERT: H 420 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7784 (tptm) REVERT: H 431 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8008 (tpp-160) REVERT: H 484 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: I 75 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7985 (tp) REVERT: I 88 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8690 (mm) REVERT: I 138 ASN cc_start: 0.8869 (t0) cc_final: 0.8455 (t0) REVERT: I 170 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8473 (mt) REVERT: I 271 ARG cc_start: 0.6650 (mmt90) cc_final: 0.6425 (mmt90) REVERT: I 431 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8140 (tpp-160) REVERT: J 138 ASN cc_start: 0.8736 (t0) cc_final: 0.8415 (t0) REVERT: J 312 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8258 (ptpt) REVERT: J 431 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7782 (tpp-160) REVERT: J 537 ASP cc_start: 0.8378 (m-30) cc_final: 0.7760 (m-30) REVERT: K 31 GLU cc_start: 0.7237 (pm20) cc_final: 0.6912 (pm20) REVERT: K 62 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7989 (mtt180) REVERT: K 102 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8128 (mt-10) REVERT: K 170 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8521 (mt) REVERT: K 420 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8001 (tttm) REVERT: K 431 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.7981 (tpp-160) REVERT: L 31 GLU cc_start: 0.7154 (pm20) cc_final: 0.6845 (pm20) REVERT: L 89 LYS cc_start: 0.8761 (tppt) cc_final: 0.8427 (ttpt) REVERT: L 102 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7875 (mt-10) REVERT: L 138 ASN cc_start: 0.8824 (t0) cc_final: 0.8482 (t0) REVERT: L 192 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.7994 (ppp) REVERT: L 271 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6279 (mpt-90) REVERT: L 420 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7773 (tptm) REVERT: L 431 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.7970 (tpp-160) REVERT: L 484 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8489 (tp30) REVERT: M 88 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8676 (mm) REVERT: M 89 LYS cc_start: 0.8565 (tppt) cc_final: 0.8227 (tttt) REVERT: M 138 ASN cc_start: 0.8824 (t0) cc_final: 0.8508 (t0) REVERT: M 155 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8242 (tp30) REVERT: M 170 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8422 (mt) REVERT: M 192 MET cc_start: 0.9101 (ppp) cc_final: 0.8534 (ppp) REVERT: M 278 GLU cc_start: 0.4757 (OUTLIER) cc_final: 0.3908 (mm-30) REVERT: M 387 TYR cc_start: 0.2238 (OUTLIER) cc_final: 0.1640 (m-80) REVERT: N 102 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8121 (mt-10) REVERT: N 138 ASN cc_start: 0.8864 (t0) cc_final: 0.8441 (t0) REVERT: N 170 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8262 (mt) REVERT: N 337 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8016 (mtmt) REVERT: N 420 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7962 (tttp) REVERT: N 431 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7958 (mmm160) outliers start: 407 outliers final: 254 residues processed: 944 average time/residue: 0.6531 time to fit residues: 1052.5862 Evaluate side-chains 855 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 289 poor density : 566 time to evaluate : 6.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 420 LYS Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 420 LYS Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 387 TYR Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 254 SER Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 411 SER Chi-restraints excluded: chain H residue 420 LYS Chi-restraints excluded: chain H residue 435 GLU Chi-restraints excluded: chain H residue 470 ILE Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 259 ILE Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 450 SER Chi-restraints excluded: chain I residue 470 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 241 PHE Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 326 VAL Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain J residue 470 ILE Chi-restraints excluded: chain J residue 471 ILE Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 520 ILE Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 327 PHE Chi-restraints excluded: chain K residue 349 ILE Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 411 SER Chi-restraints excluded: chain K residue 420 LYS Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain K residue 470 ILE Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 267 HIS Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 406 ILE Chi-restraints excluded: chain L residue 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 470 ILE Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 492 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 278 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 373 GLU Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 470 ILE Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain M residue 545 LEU Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 170 ILE Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 254 SER Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 387 TYR Chi-restraints excluded: chain N residue 406 ILE Chi-restraints excluded: chain N residue 411 SER Chi-restraints excluded: chain N residue 420 LYS Chi-restraints excluded: chain N residue 470 ILE Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 492 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 541 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 8.9990 chunk 399 optimal weight: 40.0000 chunk 10 optimal weight: 3.9990 chunk 523 optimal weight: 3.9990 chunk 290 optimal weight: 30.0000 chunk 600 optimal weight: 20.0000 chunk 486 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 0.7980 chunk 631 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 172 GLN I 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 55272 Z= 0.275 Angle : 0.562 9.061 74620 Z= 0.292 Chirality : 0.042 0.232 9086 Planarity : 0.003 0.052 9702 Dihedral : 4.014 56.842 7742 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 7.50 % Allowed : 34.38 % Favored : 58.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 7364 helix: 1.47 (0.08), residues: 4060 sheet: -1.80 (0.17), residues: 798 loop : -1.38 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 29 PHE 0.023 0.001 PHE I 225 TYR 0.004 0.001 TYR K 387 ARG 0.009 0.000 ARG H 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 438 poor density : 595 time to evaluate : 6.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7199 (pm20) cc_final: 0.6908 (pm20) REVERT: A 89 LYS cc_start: 0.8813 (tppt) cc_final: 0.8374 (ttpt) REVERT: A 102 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7552 (tm-30) REVERT: A 271 ARG cc_start: 0.6345 (mmt90) cc_final: 0.6068 (mmt90) REVERT: A 312 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8629 (ptpt) REVERT: A 342 MET cc_start: 0.5310 (pmm) cc_final: 0.5092 (pmm) REVERT: A 420 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7748 (tptm) REVERT: A 431 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8019 (tpp-160) REVERT: B 31 GLU cc_start: 0.7185 (pm20) cc_final: 0.6839 (pm20) REVERT: B 75 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8069 (tp) REVERT: B 88 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 89 LYS cc_start: 0.8684 (tppt) cc_final: 0.8183 (ttpt) REVERT: B 138 ASN cc_start: 0.8875 (t0) cc_final: 0.8498 (t0) REVERT: B 170 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8654 (mt) REVERT: B 337 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7843 (mtmt) REVERT: B 407 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8691 (mmmm) REVERT: B 431 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8158 (tpp-160) REVERT: C 100 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8687 (mt) REVERT: C 102 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: C 420 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7708 (tptm) REVERT: C 431 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7889 (tpp-160) REVERT: C 537 ASP cc_start: 0.8391 (m-30) cc_final: 0.7785 (m-30) REVERT: D 31 GLU cc_start: 0.7320 (pm20) cc_final: 0.6943 (pm20) REVERT: D 62 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8017 (mtt180) REVERT: D 278 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.3856 (mm-30) REVERT: D 431 ARG cc_start: 0.8595 (mmm-85) cc_final: 0.8011 (tpp-160) REVERT: E 31 GLU cc_start: 0.7202 (pm20) cc_final: 0.6896 (pm20) REVERT: E 192 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7787 (ppp) REVERT: E 271 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6434 (mmt90) REVERT: E 337 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8094 (mtpp) REVERT: E 373 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5237 (tp30) REVERT: E 420 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7733 (tptm) REVERT: E 431 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.7984 (mmp80) REVERT: F 75 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8029 (tp) REVERT: F 88 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8680 (mm) REVERT: F 89 LYS cc_start: 0.8611 (tppt) cc_final: 0.8339 (tttt) REVERT: F 138 ASN cc_start: 0.8813 (t0) cc_final: 0.8423 (t0) REVERT: F 387 TYR cc_start: 0.2171 (OUTLIER) cc_final: 0.1625 (m-80) REVERT: F 431 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8097 (mmm160) REVERT: G 31 GLU cc_start: 0.7261 (pm20) cc_final: 0.6897 (pm20) REVERT: G 170 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8109 (mt) REVERT: G 192 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.7957 (ppp) REVERT: G 201 ILE cc_start: 0.8131 (tp) cc_final: 0.7876 (tp) REVERT: G 278 GLU cc_start: 0.5266 (OUTLIER) cc_final: 0.4610 (mm-30) REVERT: G 337 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8060 (mtmt) REVERT: G 420 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7662 (tptm) REVERT: G 517 VAL cc_start: 0.9113 (p) cc_final: 0.8771 (m) REVERT: G 537 ASP cc_start: 0.8199 (m-30) cc_final: 0.7560 (m-30) REVERT: H 31 GLU cc_start: 0.7009 (pm20) cc_final: 0.6700 (pm20) REVERT: H 89 LYS cc_start: 0.8793 (tppt) cc_final: 0.8504 (ttpt) REVERT: H 373 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5735 (tp30) REVERT: H 420 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7780 (tptm) REVERT: H 431 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.8019 (tpp-160) REVERT: H 484 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: I 31 GLU cc_start: 0.7266 (pm20) cc_final: 0.6943 (pm20) REVERT: I 75 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7997 (tp) REVERT: I 88 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8679 (mm) REVERT: I 102 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8107 (mt-10) REVERT: I 271 ARG cc_start: 0.6643 (mmt90) cc_final: 0.6422 (mmt90) REVERT: I 278 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.4565 (mm-30) REVERT: I 431 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8188 (tpp-160) REVERT: J 31 GLU cc_start: 0.7221 (pm20) cc_final: 0.6888 (pm20) REVERT: J 138 ASN cc_start: 0.8725 (t0) cc_final: 0.8396 (t0) REVERT: J 312 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8259 (ptpt) REVERT: J 431 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7731 (tpp-160) REVERT: J 537 ASP cc_start: 0.8375 (m-30) cc_final: 0.7763 (m-30) REVERT: K 31 GLU cc_start: 0.7308 (pm20) cc_final: 0.6950 (pm20) REVERT: K 62 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8019 (mtt180) REVERT: K 102 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8126 (mt-10) REVERT: K 278 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.4505 (mm-30) REVERT: K 420 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7994 (tttm) REVERT: L 31 GLU cc_start: 0.7267 (pm20) cc_final: 0.6931 (pm20) REVERT: L 89 LYS cc_start: 0.8802 (tppt) cc_final: 0.8406 (ttpt) REVERT: L 138 ASN cc_start: 0.8805 (t0) cc_final: 0.8434 (t0) REVERT: L 192 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.7989 (ppp) REVERT: L 271 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6448 (mmt90) REVERT: L 420 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7762 (tptm) REVERT: L 431 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.7995 (tpp-160) REVERT: M 31 GLU cc_start: 0.6790 (pm20) cc_final: 0.6448 (pm20) REVERT: M 75 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7955 (tp) REVERT: M 88 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8682 (mm) REVERT: M 89 LYS cc_start: 0.8595 (tppt) cc_final: 0.8221 (tttt) REVERT: M 138 ASN cc_start: 0.8825 (t0) cc_final: 0.8492 (t0) REVERT: M 155 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8272 (tp30) REVERT: M 170 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8610 (mt) REVERT: M 278 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.3896 (mm-30) REVERT: M 387 TYR cc_start: 0.2034 (OUTLIER) cc_final: 0.1423 (m-10) REVERT: N 102 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: N 138 ASN cc_start: 0.8864 (t0) cc_final: 0.8442 (t0) REVERT: N 170 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8428 (mt) REVERT: N 337 LYS cc_start: 0.8265 (ttmm) cc_final: 0.8042 (mtmt) REVERT: N 420 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7950 (tttp) REVERT: N 431 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.7988 (mmm160) outliers start: 438 outliers final: 322 residues processed: 978 average time/residue: 0.6142 time to fit residues: 1021.3779 Evaluate side-chains 924 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 362 poor density : 562 time to evaluate : 6.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 420 LYS Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain F residue 29 HIS Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 420 LYS Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 387 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 254 SER Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 327 PHE Chi-restraints excluded: chain H residue 373 GLU Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 411 SER Chi-restraints excluded: chain H residue 420 LYS Chi-restraints excluded: chain H residue 435 GLU Chi-restraints excluded: chain H residue 450 SER Chi-restraints excluded: chain H residue 470 ILE Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 259 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 LYS Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 450 SER Chi-restraints excluded: chain I residue 470 ILE Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 241 PHE Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain J residue 427 LEU Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain J residue 470 ILE Chi-restraints excluded: chain J residue 471 ILE Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 520 ILE Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 241 PHE Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 327 PHE Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 411 SER Chi-restraints excluded: chain K residue 420 LYS Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain K residue 470 ILE Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 520 ILE Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 267 HIS Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 450 SER Chi-restraints excluded: chain L residue 470 ILE Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 241 PHE Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 254 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 278 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 373 GLU Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 470 ILE Chi-restraints excluded: chain M residue 520 ILE Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain M residue 545 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 170 ILE Chi-restraints excluded: chain N residue 254 SER Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 373 GLU Chi-restraints excluded: chain N residue 387 TYR Chi-restraints excluded: chain N residue 411 SER Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 420 LYS Chi-restraints excluded: chain N residue 450 SER Chi-restraints excluded: chain N residue 470 ILE Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 492 VAL Chi-restraints excluded: chain N residue 520 ILE Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 541 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 6.9990 chunk 633 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 413 optimal weight: 5.9990 chunk 173 optimal weight: 0.4980 chunk 704 optimal weight: 20.0000 chunk 584 optimal weight: 1.9990 chunk 326 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 232 optimal weight: 0.1980 chunk 369 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 55272 Z= 0.145 Angle : 0.526 9.606 74620 Z= 0.272 Chirality : 0.042 0.414 9086 Planarity : 0.003 0.044 9702 Dihedral : 3.683 18.187 7734 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.07 % Allowed : 37.38 % Favored : 57.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 7364 helix: 1.72 (0.08), residues: 4060 sheet: -1.65 (0.16), residues: 798 loop : -1.36 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 29 PHE 0.025 0.001 PHE I 225 TYR 0.005 0.001 TYR D 156 ARG 0.007 0.000 ARG L 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 655 time to evaluate : 6.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 HIS cc_start: 0.6345 (OUTLIER) cc_final: 0.6138 (t-90) REVERT: A 31 GLU cc_start: 0.7013 (pm20) cc_final: 0.6737 (pm20) REVERT: A 89 LYS cc_start: 0.8850 (tppt) cc_final: 0.8413 (ttpt) REVERT: A 312 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8581 (ptpt) REVERT: A 420 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7751 (tptm) REVERT: A 431 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.7971 (tpp-160) REVERT: B 31 GLU cc_start: 0.7065 (pm20) cc_final: 0.6768 (pm20) REVERT: B 88 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8508 (mm) REVERT: B 89 LYS cc_start: 0.8562 (tppt) cc_final: 0.8168 (ttpt) REVERT: B 138 ASN cc_start: 0.8746 (t0) cc_final: 0.8067 (t0) REVERT: B 172 GLN cc_start: 0.8464 (tt0) cc_final: 0.8010 (tp-100) REVERT: B 334 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7961 (tppt) REVERT: B 337 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7955 (mtmt) REVERT: B 373 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6153 (pt0) REVERT: B 407 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8651 (mmmm) REVERT: B 431 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8111 (tpp-160) REVERT: C 31 GLU cc_start: 0.7113 (pm20) cc_final: 0.6864 (pm20) REVERT: C 102 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: C 420 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7749 (tptm) REVERT: C 431 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7820 (tpp-160) REVERT: C 537 ASP cc_start: 0.8474 (m-30) cc_final: 0.7839 (m-30) REVERT: D 31 GLU cc_start: 0.7266 (pm20) cc_final: 0.6920 (pm20) REVERT: D 278 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.3945 (mm-30) REVERT: D 431 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.7965 (tpp-160) REVERT: D 481 MET cc_start: 0.8826 (mmt) cc_final: 0.8608 (mmt) REVERT: D 554 GLU cc_start: 0.7372 (pt0) cc_final: 0.7094 (pt0) REVERT: E 31 GLU cc_start: 0.7127 (pm20) cc_final: 0.6856 (pm20) REVERT: E 192 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7933 (ppp) REVERT: E 271 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6185 (mmt90) REVERT: E 420 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7686 (tptm) REVERT: E 431 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.7956 (mmp80) REVERT: F 89 LYS cc_start: 0.8591 (tppt) cc_final: 0.8315 (tttt) REVERT: F 138 ASN cc_start: 0.8671 (t0) cc_final: 0.8241 (t0) REVERT: F 192 MET cc_start: 0.8731 (ppp) cc_final: 0.8219 (ppp) REVERT: F 271 ARG cc_start: 0.6776 (mpt180) cc_final: 0.6369 (mmt90) REVERT: F 326 VAL cc_start: 0.5579 (OUTLIER) cc_final: 0.5313 (m) REVERT: F 387 TYR cc_start: 0.2349 (OUTLIER) cc_final: 0.1805 (m-80) REVERT: F 431 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.8146 (tpp80) REVERT: G 31 GLU cc_start: 0.7105 (pm20) cc_final: 0.6714 (pm20) REVERT: G 100 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8706 (mt) REVERT: G 170 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8028 (mt) REVERT: G 192 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8067 (ppp) REVERT: G 201 ILE cc_start: 0.8139 (tp) cc_final: 0.7863 (tp) REVERT: G 278 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4636 (mm-30) REVERT: G 337 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7922 (mtmt) REVERT: G 342 MET cc_start: 0.4588 (pmm) cc_final: 0.4379 (pmm) REVERT: G 420 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7649 (tptm) REVERT: G 431 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7916 (tpp-160) REVERT: G 537 ASP cc_start: 0.8187 (m-30) cc_final: 0.7544 (m-30) REVERT: H 31 GLU cc_start: 0.6997 (pm20) cc_final: 0.6715 (pm20) REVERT: H 89 LYS cc_start: 0.8800 (tppt) cc_final: 0.8507 (ttpt) REVERT: H 354 GLU cc_start: 0.8185 (mp0) cc_final: 0.7957 (mp0) REVERT: H 420 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7785 (tptm) REVERT: H 431 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.7983 (tpp-160) REVERT: I 31 GLU cc_start: 0.7256 (pm20) cc_final: 0.6993 (pm20) REVERT: I 88 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8455 (mm) REVERT: I 102 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8078 (mt-10) REVERT: I 271 ARG cc_start: 0.6689 (mmt90) cc_final: 0.6478 (mmt90) REVERT: I 431 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.8150 (tpp-160) REVERT: J 31 GLU cc_start: 0.7090 (pm20) cc_final: 0.6820 (pm20) REVERT: J 100 LEU cc_start: 0.8842 (mt) cc_final: 0.8621 (mt) REVERT: J 102 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: J 138 ASN cc_start: 0.8612 (t0) cc_final: 0.8270 (t0) REVERT: J 192 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8015 (ppp) REVERT: J 312 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8147 (ptpt) REVERT: J 358 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8515 (pt) REVERT: J 431 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7678 (tpp-160) REVERT: J 537 ASP cc_start: 0.8421 (m-30) cc_final: 0.7806 (m-30) REVERT: K 31 GLU cc_start: 0.7220 (pm20) cc_final: 0.6906 (pm20) REVERT: K 102 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: K 163 ASP cc_start: 0.7168 (t0) cc_final: 0.6968 (t0) REVERT: K 278 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.4441 (mm-30) REVERT: K 420 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8039 (ttpt) REVERT: K 431 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.7950 (tpp-160) REVERT: L 31 GLU cc_start: 0.7132 (pm20) cc_final: 0.6836 (pm20) REVERT: L 89 LYS cc_start: 0.8787 (tppt) cc_final: 0.8388 (ttpt) REVERT: L 138 ASN cc_start: 0.8747 (t0) cc_final: 0.8360 (t0) REVERT: L 192 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8000 (ppp) REVERT: L 271 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6472 (mmt90) REVERT: L 420 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7768 (tptm) REVERT: L 431 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.7983 (tpp-160) REVERT: M 31 GLU cc_start: 0.6748 (pm20) cc_final: 0.6499 (pm20) REVERT: M 138 ASN cc_start: 0.8723 (t0) cc_final: 0.8372 (t0) REVERT: M 155 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8236 (tp30) REVERT: M 192 MET cc_start: 0.8806 (ppp) cc_final: 0.8276 (ppp) REVERT: M 387 TYR cc_start: 0.2226 (OUTLIER) cc_final: 0.1632 (m-10) REVERT: M 431 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.7940 (tpp-160) REVERT: M 554 GLU cc_start: 0.7748 (pt0) cc_final: 0.7521 (pt0) REVERT: N 29 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.6248 (t-90) REVERT: N 100 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8653 (mt) REVERT: N 102 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: N 138 ASN cc_start: 0.8743 (t0) cc_final: 0.8326 (t0) REVERT: N 337 LYS cc_start: 0.8275 (ttmm) cc_final: 0.8045 (mtmt) REVERT: N 420 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7633 (tptm) outliers start: 296 outliers final: 189 residues processed: 882 average time/residue: 0.6236 time to fit residues: 936.3784 Evaluate side-chains 831 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 608 time to evaluate : 6.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 420 LYS Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain F residue 29 HIS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 LYS Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 387 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 411 SER Chi-restraints excluded: chain H residue 420 LYS Chi-restraints excluded: chain H residue 435 GLU Chi-restraints excluded: chain H residue 450 SER Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 LYS Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 427 LEU Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 420 LYS Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 373 GLU Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain N residue 29 HIS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 246 ILE Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 387 TYR Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 420 LYS Chi-restraints excluded: chain N residue 435 GLU Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 541 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 401 optimal weight: 40.0000 chunk 514 optimal weight: 0.0170 chunk 398 optimal weight: 6.9990 chunk 592 optimal weight: 0.0370 chunk 393 optimal weight: 8.9990 chunk 701 optimal weight: 50.0000 chunk 439 optimal weight: 7.9990 chunk 427 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 overall best weight: 3.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55272 Z= 0.223 Angle : 0.553 10.883 74620 Z= 0.284 Chirality : 0.042 0.274 9086 Planarity : 0.003 0.044 9702 Dihedral : 3.685 17.293 7728 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.74 % Allowed : 37.10 % Favored : 57.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 7364 helix: 1.70 (0.08), residues: 4060 sheet: -1.54 (0.17), residues: 770 loop : -1.36 (0.11), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS K 29 PHE 0.024 0.001 PHE I 225 TYR 0.003 0.000 TYR F 387 ARG 0.006 0.000 ARG L 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 335 poor density : 612 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.6052 (t-170) REVERT: A 31 GLU cc_start: 0.7144 (pm20) cc_final: 0.6831 (pm20) REVERT: A 102 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 271 ARG cc_start: 0.6101 (mmt90) cc_final: 0.5745 (mmt90) REVERT: A 312 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8581 (ptpt) REVERT: A 420 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7721 (tptm) REVERT: A 431 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.7990 (tpp-160) REVERT: B 31 GLU cc_start: 0.7156 (pm20) cc_final: 0.6831 (pm20) REVERT: B 88 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8597 (mm) REVERT: B 89 LYS cc_start: 0.8668 (tppt) cc_final: 0.8188 (ttpt) REVERT: B 138 ASN cc_start: 0.8788 (t0) cc_final: 0.8321 (t0) REVERT: B 172 GLN cc_start: 0.8439 (tt0) cc_final: 0.7973 (tp-100) REVERT: B 271 ARG cc_start: 0.6635 (mmt90) cc_final: 0.6389 (mmt90) REVERT: B 337 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7825 (mtmt) REVERT: B 373 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6169 (pt0) REVERT: B 407 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8684 (mmmm) REVERT: B 431 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8162 (tpp-160) REVERT: C 31 GLU cc_start: 0.7112 (pm20) cc_final: 0.6823 (pm20) REVERT: C 102 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: C 420 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7733 (tptm) REVERT: C 431 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7870 (tpp-160) REVERT: C 537 ASP cc_start: 0.8463 (m-30) cc_final: 0.7825 (m-30) REVERT: D 31 GLU cc_start: 0.7262 (pm20) cc_final: 0.6847 (pm20) REVERT: D 62 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7593 (mtt180) REVERT: D 161 LYS cc_start: 0.7864 (pptt) cc_final: 0.7493 (pptt) REVERT: D 163 ASP cc_start: 0.6962 (t0) cc_final: 0.6706 (t0) REVERT: D 278 GLU cc_start: 0.5077 (OUTLIER) cc_final: 0.3992 (mm-30) REVERT: D 431 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.7992 (tpp-160) REVERT: E 31 GLU cc_start: 0.7189 (pm20) cc_final: 0.6868 (pm20) REVERT: E 192 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7957 (ppp) REVERT: E 271 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6225 (mmt90) REVERT: E 373 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5260 (tp30) REVERT: E 420 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7720 (tptm) REVERT: E 431 ARG cc_start: 0.8551 (mmm-85) cc_final: 0.8082 (tpp-160) REVERT: F 89 LYS cc_start: 0.8635 (tppt) cc_final: 0.8394 (tttt) REVERT: F 138 ASN cc_start: 0.8713 (t0) cc_final: 0.8311 (t0) REVERT: F 387 TYR cc_start: 0.2152 (OUTLIER) cc_final: 0.1601 (m-80) REVERT: F 431 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8267 (tpp80) REVERT: G 31 GLU cc_start: 0.7186 (pm20) cc_final: 0.6738 (pm20) REVERT: G 100 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8709 (mt) REVERT: G 170 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8079 (mt) REVERT: G 192 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8024 (ppp) REVERT: G 201 ILE cc_start: 0.8158 (tp) cc_final: 0.7891 (tp) REVERT: G 271 ARG cc_start: 0.6173 (mmt90) cc_final: 0.5957 (mmt90) REVERT: G 278 GLU cc_start: 0.5283 (OUTLIER) cc_final: 0.4587 (mm-30) REVERT: G 420 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7671 (tptm) REVERT: G 431 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.7933 (tpp-160) REVERT: G 537 ASP cc_start: 0.8194 (m-30) cc_final: 0.7562 (m-30) REVERT: H 31 GLU cc_start: 0.7098 (pm20) cc_final: 0.6778 (pm20) REVERT: H 89 LYS cc_start: 0.8850 (tppt) cc_final: 0.8542 (ttpt) REVERT: H 102 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7483 (tm-30) REVERT: H 155 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8356 (tp30) REVERT: H 373 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5680 (tp30) REVERT: H 420 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7780 (tptm) REVERT: H 431 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.7998 (tpp-160) REVERT: I 31 GLU cc_start: 0.7285 (pm20) cc_final: 0.6984 (pm20) REVERT: I 88 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8564 (mm) REVERT: I 102 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: I 278 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.4529 (mm-30) REVERT: I 431 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8238 (tpp-160) REVERT: J 31 GLU cc_start: 0.7152 (pm20) cc_final: 0.6857 (pm20) REVERT: J 102 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: J 312 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8241 (ptpt) REVERT: J 358 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8523 (pt) REVERT: J 431 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7704 (tpp-160) REVERT: J 537 ASP cc_start: 0.8423 (m-30) cc_final: 0.7811 (m-30) REVERT: K 31 GLU cc_start: 0.7274 (pm20) cc_final: 0.6921 (pm20) REVERT: K 102 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: K 278 GLU cc_start: 0.5452 (OUTLIER) cc_final: 0.4448 (mm-30) REVERT: K 373 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5755 (pt0) REVERT: K 431 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.7967 (tpp-160) REVERT: L 31 GLU cc_start: 0.7218 (pm20) cc_final: 0.6883 (pm20) REVERT: L 89 LYS cc_start: 0.8805 (tppt) cc_final: 0.8401 (ttpt) REVERT: L 192 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8027 (ppp) REVERT: L 271 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6445 (mmt90) REVERT: L 420 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7761 (tptm) REVERT: L 431 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.8015 (tpp-160) REVERT: M 31 GLU cc_start: 0.6831 (pm20) cc_final: 0.6572 (pm20) REVERT: M 138 ASN cc_start: 0.8780 (t0) cc_final: 0.8403 (t0) REVERT: M 155 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8252 (tp30) REVERT: M 278 GLU cc_start: 0.4774 (OUTLIER) cc_final: 0.3851 (mm-30) REVERT: M 387 TYR cc_start: 0.1997 (OUTLIER) cc_final: 0.1401 (m-10) REVERT: M 431 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.7962 (tpp-160) REVERT: M 554 GLU cc_start: 0.7808 (pt0) cc_final: 0.7603 (pt0) REVERT: N 100 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8656 (mt) REVERT: N 102 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: N 317 ASP cc_start: 0.6963 (m-30) cc_final: 0.6749 (t0) REVERT: N 337 LYS cc_start: 0.8289 (ttmm) cc_final: 0.8063 (mtmt) REVERT: N 420 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7611 (tptm) REVERT: N 537 ASP cc_start: 0.8174 (m-30) cc_final: 0.7485 (m-30) outliers start: 335 outliers final: 249 residues processed: 884 average time/residue: 0.6212 time to fit residues: 935.2367 Evaluate side-chains 881 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 286 poor density : 595 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 420 LYS Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain F residue 29 HIS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 420 LYS Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 387 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 326 VAL Chi-restraints excluded: chain H residue 373 GLU Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 411 SER Chi-restraints excluded: chain H residue 420 LYS Chi-restraints excluded: chain H residue 435 GLU Chi-restraints excluded: chain H residue 450 SER Chi-restraints excluded: chain H residue 470 ILE Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 LYS Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 450 SER Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain J residue 427 LEU Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 411 SER Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain K residue 470 ILE Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 267 HIS Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 450 SER Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 254 SER Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 278 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 373 GLU Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 246 ILE Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 373 GLU Chi-restraints excluded: chain N residue 387 TYR Chi-restraints excluded: chain N residue 411 SER Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 420 LYS Chi-restraints excluded: chain N residue 450 SER Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 492 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 8.9990 chunk 280 optimal weight: 8.9990 chunk 419 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 446 optimal weight: 0.4980 chunk 478 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 551 optimal weight: 40.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 55272 Z= 0.297 Angle : 0.600 12.286 74620 Z= 0.309 Chirality : 0.043 0.236 9086 Planarity : 0.003 0.045 9702 Dihedral : 3.843 17.385 7728 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 6.61 % Allowed : 36.43 % Favored : 56.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7364 helix: 1.59 (0.08), residues: 4060 sheet: -1.68 (0.17), residues: 798 loop : -1.38 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 29 PHE 0.021 0.001 PHE I 225 TYR 0.004 0.001 TYR J 387 ARG 0.006 0.000 ARG L 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 386 poor density : 599 time to evaluate : 6.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7015 (pm20) cc_final: 0.6689 (pm20) REVERT: A 89 LYS cc_start: 0.8833 (tppt) cc_final: 0.8443 (ttpt) REVERT: A 102 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: A 271 ARG cc_start: 0.6035 (mmt90) cc_final: 0.5698 (mmt90) REVERT: A 312 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8623 (ptpt) REVERT: A 420 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7706 (tptm) REVERT: A 431 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8013 (tpp-160) REVERT: B 31 GLU cc_start: 0.7291 (pm20) cc_final: 0.6953 (pm20) REVERT: B 88 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8790 (mm) REVERT: B 89 LYS cc_start: 0.8740 (tppt) cc_final: 0.8204 (ttmt) REVERT: B 138 ASN cc_start: 0.8842 (t0) cc_final: 0.8482 (t0) REVERT: B 172 GLN cc_start: 0.8506 (tt0) cc_final: 0.8038 (tp-100) REVERT: B 337 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7895 (mtmt) REVERT: B 407 LYS cc_start: 0.9254 (mmmt) cc_final: 0.8697 (mmmm) REVERT: B 431 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.8199 (tpp-160) REVERT: C 31 GLU cc_start: 0.7248 (pm20) cc_final: 0.6941 (pm20) REVERT: C 102 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: C 420 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7662 (tptm) REVERT: C 431 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7867 (tpp-160) REVERT: C 537 ASP cc_start: 0.8402 (m-30) cc_final: 0.7781 (m-30) REVERT: D 31 GLU cc_start: 0.7394 (pm20) cc_final: 0.6967 (pm20) REVERT: D 62 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7715 (mtt180) REVERT: D 102 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: D 278 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.3955 (mm-30) REVERT: D 431 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8050 (tpp-160) REVERT: E 31 GLU cc_start: 0.7272 (pm20) cc_final: 0.6939 (pm20) REVERT: E 192 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.7952 (ppp) REVERT: E 223 ARG cc_start: 0.7098 (tpp80) cc_final: 0.6616 (tpp80) REVERT: E 271 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.6067 (mmt90) REVERT: E 373 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.5296 (tp30) REVERT: E 420 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7784 (tptm) REVERT: E 431 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8082 (tpp-160) REVERT: F 89 LYS cc_start: 0.8687 (tppt) cc_final: 0.8422 (tttt) REVERT: F 138 ASN cc_start: 0.8809 (t0) cc_final: 0.8409 (t0) REVERT: F 271 ARG cc_start: 0.6813 (mpt180) cc_final: 0.6267 (mmt90) REVERT: F 387 TYR cc_start: 0.2197 (OUTLIER) cc_final: 0.1642 (m-80) REVERT: F 431 ARG cc_start: 0.8592 (mmm-85) cc_final: 0.8163 (mmm160) REVERT: G 31 GLU cc_start: 0.7245 (pm20) cc_final: 0.6793 (pm20) REVERT: G 100 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8738 (mt) REVERT: G 170 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8144 (mt) REVERT: G 192 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7954 (ppp) REVERT: G 278 GLU cc_start: 0.5396 (OUTLIER) cc_final: 0.4685 (mm-30) REVERT: G 517 VAL cc_start: 0.9079 (p) cc_final: 0.8840 (m) REVERT: G 537 ASP cc_start: 0.8211 (m-30) cc_final: 0.7575 (m-30) REVERT: H 31 GLU cc_start: 0.7041 (pm20) cc_final: 0.6714 (pm20) REVERT: H 89 LYS cc_start: 0.8864 (tppt) cc_final: 0.8540 (ttmt) REVERT: H 102 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7550 (tm-30) REVERT: H 373 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5814 (tp30) REVERT: H 420 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7780 (tptm) REVERT: H 431 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8020 (tpp-160) REVERT: H 526 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8401 (t0) REVERT: I 31 GLU cc_start: 0.7178 (pm20) cc_final: 0.6871 (pm20) REVERT: I 75 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8045 (tp) REVERT: I 88 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8738 (mm) REVERT: I 102 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: I 278 GLU cc_start: 0.5480 (OUTLIER) cc_final: 0.4505 (mm-30) REVERT: I 431 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8250 (tpp-160) REVERT: J 31 GLU cc_start: 0.7224 (pm20) cc_final: 0.6881 (pm20) REVERT: J 89 LYS cc_start: 0.8555 (tppt) cc_final: 0.8016 (tttp) REVERT: J 138 ASN cc_start: 0.8704 (t0) cc_final: 0.8345 (t0) REVERT: J 357 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8042 (mm) REVERT: J 358 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8510 (pt) REVERT: J 431 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7727 (tpp-160) REVERT: J 537 ASP cc_start: 0.8382 (m-30) cc_final: 0.7772 (m-30) REVERT: K 31 GLU cc_start: 0.7370 (pm20) cc_final: 0.6998 (pm20) REVERT: K 278 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4398 (mm-30) REVERT: K 373 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5782 (pt0) REVERT: K 431 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.7952 (tpp-160) REVERT: L 31 GLU cc_start: 0.7288 (pm20) cc_final: 0.6937 (pm20) REVERT: L 89 LYS cc_start: 0.8803 (tppt) cc_final: 0.8390 (ttpt) REVERT: L 138 ASN cc_start: 0.8774 (t0) cc_final: 0.8412 (t0) REVERT: L 192 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8011 (ppp) REVERT: L 271 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6424 (mmt90) REVERT: L 420 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7754 (tptm) REVERT: L 431 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8076 (tpp-160) REVERT: M 31 GLU cc_start: 0.6959 (pm20) cc_final: 0.6656 (pm20) REVERT: M 138 ASN cc_start: 0.8831 (t0) cc_final: 0.8515 (t0) REVERT: M 192 MET cc_start: 0.8827 (ppp) cc_final: 0.8296 (ppp) REVERT: M 217 GLU cc_start: 0.6905 (tp30) cc_final: 0.6672 (tp30) REVERT: M 278 GLU cc_start: 0.4560 (OUTLIER) cc_final: 0.3661 (mm-30) REVERT: M 387 TYR cc_start: 0.2045 (OUTLIER) cc_final: 0.1439 (m-80) REVERT: M 431 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8311 (tpp80) REVERT: N 100 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8666 (mt) REVERT: N 102 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: N 278 GLU cc_start: 0.5151 (OUTLIER) cc_final: 0.4379 (mm-30) REVERT: N 337 LYS cc_start: 0.8266 (ttmm) cc_final: 0.8030 (mtmt) REVERT: N 420 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7644 (tptm) REVERT: N 537 ASP cc_start: 0.8188 (m-30) cc_final: 0.7536 (m-30) outliers start: 386 outliers final: 281 residues processed: 920 average time/residue: 0.6213 time to fit residues: 981.3630 Evaluate side-chains 900 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 318 poor density : 582 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 183 HIS Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 420 LYS Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain E residue 492 VAL Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 420 LYS Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 387 TYR Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 373 GLU Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 411 SER Chi-restraints excluded: chain H residue 420 LYS Chi-restraints excluded: chain H residue 435 GLU Chi-restraints excluded: chain H residue 450 SER Chi-restraints excluded: chain H residue 470 ILE Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 526 ASP Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 LYS Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 450 SER Chi-restraints excluded: chain I residue 470 ILE Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 327 PHE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain J residue 427 LEU Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain J residue 470 ILE Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 520 ILE Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 260 ILE Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 411 SER Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain K residue 470 ILE Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 520 ILE Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 267 HIS Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 406 ILE Chi-restraints excluded: chain L residue 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 450 SER Chi-restraints excluded: chain L residue 470 ILE Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 150 VAL Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 254 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 278 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 373 GLU Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 470 ILE Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 240 GLU Chi-restraints excluded: chain N residue 260 ILE Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 278 GLU Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 373 GLU Chi-restraints excluded: chain N residue 387 TYR Chi-restraints excluded: chain N residue 411 SER Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 420 LYS Chi-restraints excluded: chain N residue 435 GLU Chi-restraints excluded: chain N residue 450 SER Chi-restraints excluded: chain N residue 470 ILE Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 492 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 541 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 6.9990 chunk 672 optimal weight: 8.9990 chunk 613 optimal weight: 0.0870 chunk 653 optimal weight: 8.9990 chunk 393 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 513 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 590 optimal weight: 0.8980 chunk 618 optimal weight: 0.9990 chunk 651 optimal weight: 40.0000 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS N 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 55272 Z= 0.162 Angle : 0.562 11.578 74620 Z= 0.287 Chirality : 0.042 0.260 9086 Planarity : 0.003 0.040 9702 Dihedral : 3.706 17.686 7728 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.83 % Allowed : 37.79 % Favored : 57.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.10), residues: 7364 helix: 1.79 (0.08), residues: 3976 sheet: -1.64 (0.17), residues: 798 loop : -1.31 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 29 PHE 0.019 0.001 PHE D 225 TYR 0.004 0.000 TYR J 156 ARG 0.007 0.000 ARG G 431 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 634 time to evaluate : 6.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7065 (pm20) cc_final: 0.6771 (pm20) REVERT: A 89 LYS cc_start: 0.8868 (tppt) cc_final: 0.8445 (ttpt) REVERT: A 271 ARG cc_start: 0.5949 (mmt90) cc_final: 0.5654 (mmt90) REVERT: A 312 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8583 (ptpt) REVERT: A 420 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7741 (tptm) REVERT: A 431 ARG cc_start: 0.8446 (mmm-85) cc_final: 0.7973 (tpp-160) REVERT: B 31 GLU cc_start: 0.7220 (pm20) cc_final: 0.6947 (pm20) REVERT: B 88 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8595 (mm) REVERT: B 89 LYS cc_start: 0.8614 (tppt) cc_final: 0.8206 (ttpt) REVERT: B 138 ASN cc_start: 0.8749 (t0) cc_final: 0.8259 (t0) REVERT: B 172 GLN cc_start: 0.8483 (tt0) cc_final: 0.7975 (tp-100) REVERT: B 337 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7903 (mtmt) REVERT: B 373 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6229 (pt0) REVERT: B 407 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8691 (mmmm) REVERT: B 431 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8182 (tpp-160) REVERT: C 31 GLU cc_start: 0.7078 (pm20) cc_final: 0.6805 (pm20) REVERT: C 102 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: C 420 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7648 (tptm) REVERT: C 431 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7837 (tpp-160) REVERT: C 537 ASP cc_start: 0.8428 (m-30) cc_final: 0.7788 (m-30) REVERT: D 31 GLU cc_start: 0.7296 (pm20) cc_final: 0.6903 (pm20) REVERT: D 62 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7829 (mtt180) REVERT: D 102 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: D 161 LYS cc_start: 0.7876 (pptt) cc_final: 0.7553 (pptt) REVERT: D 163 ASP cc_start: 0.6970 (t0) cc_final: 0.6687 (t0) REVERT: D 278 GLU cc_start: 0.5063 (OUTLIER) cc_final: 0.3945 (mm-30) REVERT: D 373 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5682 (tt0) REVERT: D 431 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.7993 (tpp-160) REVERT: E 31 GLU cc_start: 0.7204 (pm20) cc_final: 0.6926 (pm20) REVERT: E 192 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.7910 (ppp) REVERT: E 271 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6446 (mmt90) REVERT: E 373 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5401 (tp30) REVERT: E 420 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7726 (tptm) REVERT: E 431 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8026 (mmp80) REVERT: F 89 LYS cc_start: 0.8662 (tppt) cc_final: 0.8398 (tttt) REVERT: F 138 ASN cc_start: 0.8711 (t0) cc_final: 0.8325 (t0) REVERT: F 271 ARG cc_start: 0.6598 (mpt180) cc_final: 0.6086 (mmt90) REVERT: F 387 TYR cc_start: 0.1992 (OUTLIER) cc_final: 0.1456 (m-80) REVERT: F 431 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8273 (tpp80) REVERT: G 31 GLU cc_start: 0.7149 (pm20) cc_final: 0.6716 (pm20) REVERT: G 100 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8758 (mt) REVERT: G 192 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8038 (ppp) REVERT: G 271 ARG cc_start: 0.6134 (mmt90) cc_final: 0.5927 (mpt-90) REVERT: G 431 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.7895 (tpp-160) REVERT: G 517 VAL cc_start: 0.9071 (p) cc_final: 0.8856 (m) REVERT: G 537 ASP cc_start: 0.8185 (m-30) cc_final: 0.7543 (m-30) REVERT: H 31 GLU cc_start: 0.6966 (pm20) cc_final: 0.6670 (pm20) REVERT: H 89 LYS cc_start: 0.8803 (tppt) cc_final: 0.8546 (ttpt) REVERT: H 102 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7496 (tm-30) REVERT: H 354 GLU cc_start: 0.8190 (mp0) cc_final: 0.7947 (mp0) REVERT: H 373 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5769 (tp30) REVERT: H 420 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7785 (tptm) REVERT: H 431 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.7990 (tpp-160) REVERT: I 31 GLU cc_start: 0.7115 (pm20) cc_final: 0.6862 (pm20) REVERT: I 88 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8538 (mm) REVERT: I 102 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: I 431 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8233 (tpp-160) REVERT: I 554 GLU cc_start: 0.7689 (pt0) cc_final: 0.7458 (pt0) REVERT: J 31 GLU cc_start: 0.7006 (pm20) cc_final: 0.6707 (pm20) REVERT: J 89 LYS cc_start: 0.8566 (tppt) cc_final: 0.8010 (tttp) REVERT: J 100 LEU cc_start: 0.8795 (mt) cc_final: 0.8579 (mt) REVERT: J 358 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8540 (pt) REVERT: J 431 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7685 (tpp-160) REVERT: J 537 ASP cc_start: 0.8411 (m-30) cc_final: 0.7792 (m-30) REVERT: J 554 GLU cc_start: 0.7843 (pt0) cc_final: 0.7478 (pt0) REVERT: K 31 GLU cc_start: 0.7327 (pm20) cc_final: 0.6987 (pm20) REVERT: K 102 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: K 278 GLU cc_start: 0.5405 (OUTLIER) cc_final: 0.4386 (mm-30) REVERT: K 373 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5832 (pt0) REVERT: K 431 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.7931 (tpp-160) REVERT: L 31 GLU cc_start: 0.7107 (pm20) cc_final: 0.6794 (pm20) REVERT: L 89 LYS cc_start: 0.8827 (tppt) cc_final: 0.8452 (ttpt) REVERT: L 138 ASN cc_start: 0.8735 (t0) cc_final: 0.8365 (t0) REVERT: L 192 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8114 (ppp) REVERT: L 271 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6422 (mmt90) REVERT: L 420 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7736 (tptm) REVERT: L 431 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.8060 (tpp-160) REVERT: M 31 GLU cc_start: 0.6803 (pm20) cc_final: 0.6539 (pm20) REVERT: M 138 ASN cc_start: 0.8780 (t0) cc_final: 0.8425 (t0) REVERT: M 192 MET cc_start: 0.8850 (ppp) cc_final: 0.8187 (ppp) REVERT: M 387 TYR cc_start: 0.2094 (OUTLIER) cc_final: 0.1496 (m-10) REVERT: M 431 ARG cc_start: 0.8612 (mmm-85) cc_final: 0.7918 (tpp-160) REVERT: M 554 GLU cc_start: 0.7697 (pt0) cc_final: 0.7443 (pt0) REVERT: N 100 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8671 (mt) REVERT: N 102 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: N 138 ASN cc_start: 0.8789 (t0) cc_final: 0.8371 (t0) REVERT: N 337 LYS cc_start: 0.8263 (ttmm) cc_final: 0.8031 (mtmt) REVERT: N 420 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7568 (tptm) REVERT: N 537 ASP cc_start: 0.8160 (m-30) cc_final: 0.7468 (m-30) outliers start: 282 outliers final: 216 residues processed: 853 average time/residue: 0.6654 time to fit residues: 978.2724 Evaluate side-chains 855 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 608 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 420 LYS Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 LYS Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 387 TYR Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain G residue 435 GLU Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 373 GLU Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 411 SER Chi-restraints excluded: chain H residue 420 LYS Chi-restraints excluded: chain H residue 435 GLU Chi-restraints excluded: chain H residue 450 SER Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 LYS Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 450 SER Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain J residue 427 LEU Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 411 SER Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 406 ILE Chi-restraints excluded: chain L residue 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 450 SER Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 373 GLU Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 260 ILE Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 373 GLU Chi-restraints excluded: chain N residue 387 TYR Chi-restraints excluded: chain N residue 411 SER Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 420 LYS Chi-restraints excluded: chain N residue 435 GLU Chi-restraints excluded: chain N residue 450 SER Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 492 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 6.9990 chunk 691 optimal weight: 9.9990 chunk 422 optimal weight: 4.9990 chunk 328 optimal weight: 0.9990 chunk 480 optimal weight: 0.9980 chunk 725 optimal weight: 3.9990 chunk 667 optimal weight: 8.9990 chunk 577 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 446 optimal weight: 0.8980 chunk 354 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 55272 Z= 0.163 Angle : 0.556 12.413 74620 Z= 0.284 Chirality : 0.042 0.284 9086 Planarity : 0.003 0.038 9702 Dihedral : 3.641 17.650 7728 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.45 % Allowed : 38.16 % Favored : 57.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 7364 helix: 1.83 (0.08), residues: 3976 sheet: -1.53 (0.17), residues: 798 loop : -1.30 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 29 PHE 0.020 0.001 PHE H 225 TYR 0.004 0.000 TYR M 156 ARG 0.006 0.000 ARG G 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14728 Ramachandran restraints generated. 7364 Oldfield, 0 Emsley, 7364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 619 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7062 (pm20) cc_final: 0.6767 (pm20) REVERT: A 89 LYS cc_start: 0.8850 (tppt) cc_final: 0.8454 (ttpt) REVERT: A 269 MET cc_start: 0.5404 (mtm) cc_final: 0.4944 (ptt) REVERT: A 271 ARG cc_start: 0.6003 (mmt90) cc_final: 0.5650 (mmt90) REVERT: A 312 LYS cc_start: 0.8961 (mmtm) cc_final: 0.8575 (ptpt) REVERT: A 420 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7741 (tptm) REVERT: A 431 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.7968 (tpp-160) REVERT: B 31 GLU cc_start: 0.7224 (pm20) cc_final: 0.6942 (pm20) REVERT: B 88 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8557 (mm) REVERT: B 89 LYS cc_start: 0.8621 (tppt) cc_final: 0.8212 (ttpt) REVERT: B 138 ASN cc_start: 0.8710 (t0) cc_final: 0.8185 (t0) REVERT: B 172 GLN cc_start: 0.8485 (tt0) cc_final: 0.7990 (tp-100) REVERT: B 334 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8012 (tppt) REVERT: B 373 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6197 (pt0) REVERT: B 407 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8685 (mmmm) REVERT: B 431 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8172 (tpp-160) REVERT: C 31 GLU cc_start: 0.7116 (pm20) cc_final: 0.6878 (pm20) REVERT: C 102 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: C 420 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7649 (tptm) REVERT: C 431 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7828 (tpp-160) REVERT: C 537 ASP cc_start: 0.8507 (m-30) cc_final: 0.7871 (m-30) REVERT: D 31 GLU cc_start: 0.7362 (pm20) cc_final: 0.6961 (pm20) REVERT: D 102 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: D 161 LYS cc_start: 0.7931 (pptt) cc_final: 0.7591 (pptt) REVERT: D 163 ASP cc_start: 0.7008 (t0) cc_final: 0.6719 (t0) REVERT: D 278 GLU cc_start: 0.4923 (OUTLIER) cc_final: 0.3845 (mm-30) REVERT: D 373 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5705 (tt0) REVERT: D 431 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.7995 (tpp-160) REVERT: D 481 MET cc_start: 0.8816 (mmt) cc_final: 0.8588 (mmt) REVERT: E 31 GLU cc_start: 0.7251 (pm20) cc_final: 0.6975 (pm20) REVERT: E 192 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.7911 (ppp) REVERT: E 271 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6207 (mmt90) REVERT: E 373 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5407 (tp30) REVERT: E 420 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7717 (tptm) REVERT: E 431 ARG cc_start: 0.8547 (mmm-85) cc_final: 0.8001 (mmp80) REVERT: F 89 LYS cc_start: 0.8652 (tppt) cc_final: 0.8377 (tttt) REVERT: F 138 ASN cc_start: 0.8672 (t0) cc_final: 0.8181 (t0) REVERT: F 271 ARG cc_start: 0.6607 (mpt180) cc_final: 0.6107 (mmt90) REVERT: F 387 TYR cc_start: 0.2008 (OUTLIER) cc_final: 0.1473 (m-80) REVERT: F 431 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.8263 (tpp80) REVERT: G 31 GLU cc_start: 0.7184 (pm20) cc_final: 0.6746 (pm20) REVERT: G 100 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8708 (mt) REVERT: G 192 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8032 (ppp) REVERT: G 431 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.7906 (tpp-160) REVERT: G 537 ASP cc_start: 0.8209 (m-30) cc_final: 0.7573 (m-30) REVERT: H 31 GLU cc_start: 0.6991 (pm20) cc_final: 0.6694 (pm20) REVERT: H 89 LYS cc_start: 0.8817 (tppt) cc_final: 0.8524 (ttmt) REVERT: H 102 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7503 (tm-30) REVERT: H 155 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8254 (tp30) REVERT: H 373 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5758 (tp30) REVERT: H 420 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7680 (tptm) REVERT: H 431 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8000 (tpp-160) REVERT: I 31 GLU cc_start: 0.7336 (pm20) cc_final: 0.7082 (pm20) REVERT: I 88 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8538 (mm) REVERT: I 102 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: I 431 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.8229 (tpp-160) REVERT: J 31 GLU cc_start: 0.7066 (pm20) cc_final: 0.6764 (pm20) REVERT: J 89 LYS cc_start: 0.8596 (tppt) cc_final: 0.8066 (tttp) REVERT: J 358 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8532 (pt) REVERT: J 431 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7661 (tpp-160) REVERT: J 537 ASP cc_start: 0.8454 (m-30) cc_final: 0.7863 (m-30) REVERT: J 554 GLU cc_start: 0.7856 (pt0) cc_final: 0.7485 (pt0) REVERT: K 31 GLU cc_start: 0.7374 (pm20) cc_final: 0.7025 (pm20) REVERT: K 102 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: K 161 LYS cc_start: 0.7780 (pptt) cc_final: 0.7514 (pptt) REVERT: K 163 ASP cc_start: 0.6920 (t0) cc_final: 0.6607 (t0) REVERT: K 278 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.4550 (mm-30) REVERT: K 431 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.7904 (tpp-160) REVERT: L 31 GLU cc_start: 0.7124 (pm20) cc_final: 0.6813 (pm20) REVERT: L 89 LYS cc_start: 0.8830 (tppt) cc_final: 0.8457 (ttpt) REVERT: L 192 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8116 (ppp) REVERT: L 271 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6398 (mmt90) REVERT: L 420 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7756 (tptm) REVERT: L 431 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8032 (tpp-160) REVERT: M 31 GLU cc_start: 0.6822 (pm20) cc_final: 0.6423 (pm20) REVERT: M 138 ASN cc_start: 0.8723 (t0) cc_final: 0.8357 (t0) REVERT: M 192 MET cc_start: 0.8865 (ppp) cc_final: 0.8193 (ppp) REVERT: M 387 TYR cc_start: 0.1964 (OUTLIER) cc_final: 0.1373 (m-10) REVERT: M 431 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.7884 (tpp-160) REVERT: N 100 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8647 (mt) REVERT: N 102 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7722 (tm-30) REVERT: N 337 LYS cc_start: 0.8259 (ttmm) cc_final: 0.8044 (mtmt) REVERT: N 420 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7610 (tptm) REVERT: N 537 ASP cc_start: 0.8126 (m-30) cc_final: 0.7446 (m-30) outliers start: 260 outliers final: 212 residues processed: 825 average time/residue: 0.6255 time to fit residues: 885.7596 Evaluate side-chains 851 residues out of total 5838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 610 time to evaluate : 6.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 327 PHE Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 420 LYS Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 307 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 387 TYR Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 420 LYS Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 307 PHE Chi-restraints excluded: chain F residue 387 TYR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 420 LYS Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 307 PHE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 387 TYR Chi-restraints excluded: chain G residue 411 SER Chi-restraints excluded: chain G residue 435 GLU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 307 PHE Chi-restraints excluded: chain H residue 373 GLU Chi-restraints excluded: chain H residue 387 TYR Chi-restraints excluded: chain H residue 411 SER Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 420 LYS Chi-restraints excluded: chain H residue 435 GLU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 260 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 LYS Chi-restraints excluded: chain I residue 356 THR Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 492 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 307 PHE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 358 ILE Chi-restraints excluded: chain J residue 387 TYR Chi-restraints excluded: chain J residue 406 ILE Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain J residue 427 LEU Chi-restraints excluded: chain J residue 450 SER Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 307 PHE Chi-restraints excluded: chain K residue 387 TYR Chi-restraints excluded: chain K residue 411 SER Chi-restraints excluded: chain K residue 427 LEU Chi-restraints excluded: chain K residue 492 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 260 ILE Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain L residue 356 THR Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 387 TYR Chi-restraints excluded: chain L residue 406 ILE Chi-restraints excluded: chain L residue 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain M residue 373 GLU Chi-restraints excluded: chain M residue 387 TYR Chi-restraints excluded: chain M residue 406 ILE Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 427 LEU Chi-restraints excluded: chain M residue 450 SER Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 260 ILE Chi-restraints excluded: chain N residue 274 VAL Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 373 GLU Chi-restraints excluded: chain N residue 387 TYR Chi-restraints excluded: chain N residue 411 SER Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 420 LYS Chi-restraints excluded: chain N residue 435 GLU Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 492 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 3.9990 chunk 615 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 532 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 160 optimal weight: 0.0970 chunk 578 optimal weight: 0.1980 chunk 242 optimal weight: 10.0000 chunk 593 optimal weight: 0.0050 chunk 73 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.197222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139858 restraints weight = 88037.765| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 4.35 r_work: 0.3518 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 55272 Z= 0.154 Angle : 0.556 11.899 74620 Z= 0.283 Chirality : 0.042 0.263 9086 Planarity : 0.003 0.036 9702 Dihedral : 3.605 17.877 7728 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.52 % Allowed : 38.08 % Favored : 57.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 7364 helix: 1.85 (0.08), residues: 3976 sheet: -1.36 (0.18), residues: 770 loop : -1.28 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 267 PHE 0.019 0.001 PHE C 225 TYR 0.004 0.000 TYR M 156 ARG 0.006 0.000 ARG G 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15468.12 seconds wall clock time: 722 minutes 42.19 seconds (43362.19 seconds total)