Starting phenix.real_space_refine on Wed Sep 25 08:34:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/09_2024/8pe8_17629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/09_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_17629/09_2024/8pe8_17629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/09_2024/8pe8_17629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/09_2024/8pe8_17629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pe8_17629/09_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): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.54, per 1000 atoms: 0.21 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: 12.61 Conformation dependent library (CDL) restraints added in 6.0 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: 5.21 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: 21.03 Time building geometry restraints manager: 14.61 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: 1.210 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: 0.040 Extract box with map and model: 2.420 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 88.090 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.840 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 28 poor density : 765 time to evaluate : 6.128 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: 0.5226 time to fit residues: 692.2286 Evaluate side-chains 650 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 635 time to evaluate : 4.686 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 241 poor density : 630 time to evaluate : 4.752 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: 0.5021 time to fit residues: 703.0593 Evaluate side-chains 754 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 583 time to evaluate : 4.675 ------------------------------------------------------------------------------- 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: 0.6980 chunk 205 optimal weight: 10.0000 chunk 550 optimal weight: 8.9990 chunk 450 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 662 optimal weight: 7.9990 chunk 715 optimal weight: 6.9990 chunk 589 optimal weight: 30.0000 chunk 656 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 531 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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: 0.7742 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 55272 Z= 0.274 Angle : 0.563 9.141 74620 Z= 0.292 Chirality : 0.043 0.174 9086 Planarity : 0.004 0.071 9702 Dihedral : 4.215 59.614 7750 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.94 % Allowed : 34.31 % Favored : 58.75 % 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: 1.70 (0.08), residues: 3976 sheet: -1.39 (0.18), residues: 770 loop : -1.23 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS M 29 PHE 0.026 0.002 PHE L 221 TYR 0.004 0.001 TYR N 501 ARG 0.007 0.001 ARG N 223 *********************** 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 1008 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 405 poor density : 603 time to evaluate : 4.800 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: A 31 GLU cc_start: 0.7040 (pm20) cc_final: 0.6764 (pm20) REVERT: A 170 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8281 (mt) REVERT: A 312 LYS cc_start: 0.8956 (mmtm) cc_final: 0.8578 (ptpt) REVERT: A 420 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7760 (tptm) REVERT: A 431 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.7869 (mmt180) REVERT: B 88 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8740 (mm) REVERT: B 89 LYS cc_start: 0.8668 (tppt) cc_final: 0.8108 (ttmt) REVERT: B 138 ASN cc_start: 0.8880 (t0) cc_final: 0.8474 (t0) REVERT: B 170 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8283 (mt) REVERT: B 278 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.4606 (mm-30) REVERT: B 337 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7862 (mtmt) REVERT: B 407 LYS cc_start: 0.9316 (mmmt) cc_final: 0.8728 (mmmm) REVERT: B 431 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8032 (tpp-160) REVERT: C 88 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8801 (mm) REVERT: C 170 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8210 (mt) REVERT: C 192 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8182 (ppp) REVERT: C 431 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7685 (mmt180) REVERT: C 537 ASP cc_start: 0.8466 (m-30) cc_final: 0.7811 (m-30) REVERT: D 31 GLU cc_start: 0.7188 (pm20) cc_final: 0.6933 (pm20) REVERT: D 170 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8133 (mt) REVERT: D 420 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8005 (ttpt) REVERT: D 431 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.7897 (mmt180) REVERT: E 31 GLU cc_start: 0.7028 (pm20) cc_final: 0.6806 (pm20) REVERT: E 192 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.7821 (ppp) REVERT: E 337 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8154 (mtpp) REVERT: E 420 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7758 (tptm) REVERT: E 431 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.7884 (mmp80) REVERT: F 31 GLU cc_start: 0.6744 (pm20) cc_final: 0.6480 (pm20) REVERT: F 88 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8742 (mm) REVERT: F 89 LYS cc_start: 0.8611 (tppt) cc_final: 0.8269 (tttt) REVERT: F 138 ASN cc_start: 0.8770 (t0) cc_final: 0.8339 (t0) REVERT: F 170 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8159 (mt) REVERT: F 192 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8465 (ppp) REVERT: F 387 TYR cc_start: 0.2426 (OUTLIER) cc_final: 0.1960 (m-80) REVERT: F 431 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.8058 (tpp80) REVERT: G 31 GLU cc_start: 0.7060 (pm20) cc_final: 0.6731 (pm20) REVERT: G 138 ASN cc_start: 0.8864 (t0) cc_final: 0.8303 (t0) REVERT: G 170 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7993 (mt) REVERT: G 192 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.7810 (ppp) REVERT: G 337 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8018 (mtmt) REVERT: G 420 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7604 (tptm) REVERT: G 431 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7841 (mmt180) REVERT: G 537 ASP cc_start: 0.8201 (m-30) cc_final: 0.7584 (m-30) REVERT: H 31 GLU cc_start: 0.6992 (pm20) cc_final: 0.6715 (pm20) REVERT: H 89 LYS cc_start: 0.8744 (tppt) cc_final: 0.8358 (tttt) REVERT: H 170 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8362 (mt) REVERT: H 271 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6254 (mmt90) REVERT: H 420 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7554 (tptm) REVERT: H 431 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.7854 (tpp-160) REVERT: I 88 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8697 (mm) REVERT: I 89 LYS cc_start: 0.8717 (tppt) cc_final: 0.8151 (ttpt) REVERT: I 170 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8284 (mt) REVERT: I 278 GLU cc_start: 0.5377 (OUTLIER) cc_final: 0.4451 (mm-30) REVERT: I 431 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8108 (tpp-160) REVERT: J 88 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8842 (mm) REVERT: J 170 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8125 (mt) REVERT: J 192 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8066 (ppp) REVERT: J 312 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8223 (ptpt) REVERT: J 431 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7559 (mmt180) REVERT: J 537 ASP cc_start: 0.8440 (m-30) cc_final: 0.7837 (m-30) REVERT: K 31 GLU cc_start: 0.7124 (pm20) cc_final: 0.6894 (pm20) REVERT: K 170 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8161 (mt) REVERT: K 192 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8145 (ppp) REVERT: K 420 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7939 (tttm) REVERT: L 31 GLU cc_start: 0.7026 (pm20) cc_final: 0.6782 (pm20) REVERT: L 192 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8049 (ppp) REVERT: L 271 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6403 (mmt90) REVERT: L 420 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7781 (tptm) REVERT: L 431 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7856 (mmt180) REVERT: M 31 GLU cc_start: 0.6555 (pm20) cc_final: 0.6319 (pm20) REVERT: M 72 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7622 (p) REVERT: M 88 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8717 (mm) REVERT: M 89 LYS cc_start: 0.8525 (tppt) cc_final: 0.8171 (tttt) REVERT: M 138 ASN cc_start: 0.8765 (t0) cc_final: 0.8419 (t0) REVERT: M 155 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8330 (tp30) REVERT: M 170 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8216 (mt) REVERT: M 387 TYR cc_start: 0.2218 (OUTLIER) cc_final: 0.1724 (m-80) REVERT: N 102 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7712 (tm-30) REVERT: N 138 ASN cc_start: 0.8834 (t0) cc_final: 0.8279 (t0) REVERT: N 170 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8002 (mt) REVERT: N 337 LYS cc_start: 0.8357 (ttmm) cc_final: 0.8123 (mtmt) REVERT: N 420 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7615 (tptm) outliers start: 405 outliers final: 228 residues processed: 941 average time/residue: 0.5052 time to fit residues: 810.2424 Evaluate side-chains 847 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 579 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 95 LEU 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 254 SER 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 470 ILE Chi-restraints excluded: chain A residue 488 LEU 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 53 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 88 LEU 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 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 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 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 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 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 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 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 254 SER Chi-restraints excluded: chain D residue 307 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 53 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 307 PHE Chi-restraints excluded: chain E residue 327 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 530 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 150 VAL 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 247 LEU 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 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 53 VAL 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 254 SER 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 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 56 THR 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 170 ILE Chi-restraints excluded: chain H residue 192 MET 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 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 488 LEU 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 69 THR Chi-restraints excluded: chain I residue 88 LEU 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 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 53 VAL 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 216 THR 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 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 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 192 MET 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 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 470 ILE 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 69 THR 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 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 L residue 553 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 150 VAL 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 541 VAL Chi-restraints excluded: chain M residue 545 LEU 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 254 SER 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: 40.0000 chunk 497 optimal weight: 30.0000 chunk 343 optimal weight: 20.0000 chunk 73 optimal weight: 50.0000 chunk 316 optimal weight: 0.0470 chunk 444 optimal weight: 8.9990 chunk 664 optimal weight: 9.9990 chunk 703 optimal weight: 0.0970 chunk 347 optimal weight: 40.0000 chunk 629 optimal weight: 2.9990 chunk 189 optimal weight: 30.0000 overall best weight: 4.4282 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2187 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= 0.289 Angle : 0.564 8.089 74620 Z= 0.293 Chirality : 0.042 0.202 9086 Planarity : 0.003 0.057 9702 Dihedral : 4.237 57.050 7750 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 7.07 % Allowed : 34.52 % Favored : 58.41 % 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: 0.42 (0.09), residues: 7364 helix: 1.62 (0.08), residues: 3976 sheet: -1.54 (0.18), residues: 770 loop : -1.24 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 29 PHE 0.020 0.001 PHE G 221 TYR 0.004 0.001 TYR K 387 ARG 0.008 0.000 ARG D 376 *********************** 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 1016 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 603 time to evaluate : 4.793 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: A 31 GLU cc_start: 0.7071 (pm20) cc_final: 0.6761 (pm20) REVERT: A 170 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8294 (mt) REVERT: A 271 ARG cc_start: 0.6265 (mmt90) cc_final: 0.5872 (mmt90) REVERT: A 312 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8643 (ptpt) REVERT: A 342 MET cc_start: 0.5337 (pmm) cc_final: 0.5080 (pmm) REVERT: A 420 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7742 (tptm) REVERT: A 431 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.7926 (mmt180) REVERT: B 88 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8745 (mm) REVERT: B 89 LYS cc_start: 0.8671 (tppt) cc_final: 0.8131 (ttpt) REVERT: B 138 ASN cc_start: 0.8901 (t0) cc_final: 0.8500 (t0) REVERT: B 170 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8428 (mt) REVERT: B 337 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7863 (mtmt) REVERT: B 407 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8715 (mmmm) REVERT: B 431 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8105 (tpp-160) REVERT: B 484 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8515 (tp30) REVERT: C 62 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8280 (mtp85) REVERT: C 88 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C 102 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8087 (mt-10) REVERT: C 170 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8550 (mt) REVERT: C 431 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7851 (mmt180) REVERT: C 537 ASP cc_start: 0.8402 (m-30) cc_final: 0.7755 (m-30) REVERT: D 31 GLU cc_start: 0.7200 (pm20) cc_final: 0.6895 (pm20) REVERT: D 62 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8012 (mtt180) REVERT: D 161 LYS cc_start: 0.7986 (pptt) cc_final: 0.7608 (pptt) REVERT: D 163 ASP cc_start: 0.7318 (t0) cc_final: 0.7104 (t0) REVERT: D 170 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8462 (mt) REVERT: D 431 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.7922 (mmt180) REVERT: E 31 GLU cc_start: 0.7105 (pm20) cc_final: 0.6852 (pm20) REVERT: E 192 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7833 (ppp) REVERT: E 271 ARG cc_start: 0.6301 (mmt90) cc_final: 0.6002 (mmt90) REVERT: E 337 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8106 (mtpp) REVERT: E 420 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7718 (tptm) REVERT: E 431 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.7975 (mmp80) REVERT: F 31 GLU cc_start: 0.6820 (pm20) cc_final: 0.6446 (pm20) REVERT: F 75 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7952 (tp) REVERT: F 88 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8714 (mm) REVERT: F 89 LYS cc_start: 0.8608 (tppt) cc_final: 0.8275 (tttt) REVERT: F 138 ASN cc_start: 0.8783 (t0) cc_final: 0.8408 (t0) REVERT: F 170 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8333 (mt) REVERT: F 192 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8435 (ppp) REVERT: F 271 ARG cc_start: 0.6741 (mpt180) cc_final: 0.6244 (mmt90) REVERT: F 278 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.4043 (mm-30) REVERT: F 387 TYR cc_start: 0.2363 (OUTLIER) cc_final: 0.1850 (m-80) REVERT: F 431 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8054 (mmm160) REVERT: G 31 GLU cc_start: 0.7142 (pm20) cc_final: 0.6776 (pm20) REVERT: G 170 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8065 (mt) REVERT: G 192 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8016 (ppp) REVERT: G 337 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8015 (mtmt) REVERT: G 420 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7643 (tptm) REVERT: G 537 ASP cc_start: 0.8204 (m-30) cc_final: 0.7564 (m-30) REVERT: H 31 GLU cc_start: 0.7013 (pm20) cc_final: 0.6730 (pm20) REVERT: H 89 LYS cc_start: 0.8786 (tppt) cc_final: 0.8438 (ttpt) REVERT: H 170 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8427 (mt) REVERT: H 420 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7777 (tptm) REVERT: H 431 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.7969 (tpp-160) REVERT: I 75 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7975 (tp) REVERT: I 88 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8707 (mm) REVERT: I 138 ASN cc_start: 0.8859 (t0) cc_final: 0.8418 (t0) REVERT: I 431 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.8145 (tpp-160) REVERT: J 88 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8827 (mm) REVERT: J 170 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8471 (mt) REVERT: J 312 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8266 (ptpt) REVERT: J 431 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7753 (tpp-160) REVERT: J 537 ASP cc_start: 0.8383 (m-30) cc_final: 0.7770 (m-30) REVERT: K 31 GLU cc_start: 0.7172 (pm20) cc_final: 0.6878 (pm20) REVERT: K 161 LYS cc_start: 0.7697 (pptt) cc_final: 0.7314 (pptt) REVERT: K 170 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8415 (mt) REVERT: K 192 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.7953 (ppp) REVERT: K 271 ARG cc_start: 0.6564 (mmt90) cc_final: 0.5993 (mmt90) REVERT: K 420 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7992 (tttm) REVERT: K 431 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.7923 (mmt180) REVERT: L 31 GLU cc_start: 0.7090 (pm20) cc_final: 0.6823 (pm20) REVERT: L 192 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8075 (ppp) REVERT: L 271 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6352 (mpt-90) REVERT: L 420 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7737 (tptm) REVERT: L 431 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.7936 (mmt180) REVERT: M 31 GLU cc_start: 0.6615 (pm20) cc_final: 0.6282 (pm20) REVERT: M 72 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7708 (p) REVERT: M 75 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7910 (tp) REVERT: M 88 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8718 (mm) REVERT: M 89 LYS cc_start: 0.8594 (tppt) cc_final: 0.8174 (tttt) REVERT: M 138 ASN cc_start: 0.8808 (t0) cc_final: 0.8467 (t0) REVERT: M 170 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8368 (mt) REVERT: M 387 TYR cc_start: 0.2215 (OUTLIER) cc_final: 0.1661 (m-80) REVERT: N 102 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7740 (tm-30) REVERT: N 138 ASN cc_start: 0.8856 (t0) cc_final: 0.8409 (t0) REVERT: N 170 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8141 (mt) REVERT: N 278 GLU cc_start: 0.5134 (OUTLIER) cc_final: 0.4382 (mm-30) REVERT: N 337 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7988 (mtmt) REVERT: N 420 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7949 (tttp) REVERT: N 431 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7942 (mmm160) REVERT: N 537 ASP cc_start: 0.8188 (m-30) cc_final: 0.7534 (m-30) outliers start: 413 outliers final: 274 residues processed: 964 average time/residue: 0.4929 time to fit residues: 816.2294 Evaluate side-chains 888 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 573 time to evaluate : 4.811 ------------------------------------------------------------------------------- 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 82 VAL 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 170 ILE 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 470 ILE 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 48 THR 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 95 LEU 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 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 427 LEU 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 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 62 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 VAL 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 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 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 470 ILE Chi-restraints excluded: chain C residue 471 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 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 62 ARG 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 102 GLU 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 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 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 95 LEU 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 254 SER 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 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 521 GLN 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 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 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 170 ILE Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 241 PHE 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 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 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 53 VAL Chi-restraints excluded: chain G residue 56 THR 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 254 SER 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 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 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 95 LEU 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 247 LEU 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 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 56 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 82 VAL 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 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 307 PHE Chi-restraints excluded: chain I residue 356 THR 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 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 46 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 88 LEU Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 216 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 254 SER 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 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 J residue 553 VAL Chi-restraints excluded: chain K residue 46 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 170 ILE Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 307 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 56 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 82 VAL 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 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 470 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 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 95 LEU 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 247 LEU Chi-restraints excluded: chain M residue 254 SER 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 411 SER 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 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 95 LEU 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 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 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: 10.0000 chunk 399 optimal weight: 50.0000 chunk 10 optimal weight: 3.9990 chunk 523 optimal weight: 2.9990 chunk 290 optimal weight: 40.0000 chunk 600 optimal weight: 9.9990 chunk 486 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 1.9990 chunk 631 optimal weight: 6.9990 chunk 177 optimal weight: 30.0000 overall best weight: 3.2002 ------------------------------------------------------------------------------- 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: 0.7745 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 55272 Z= 0.225 Angle : 0.541 9.518 74620 Z= 0.280 Chirality : 0.042 0.259 9086 Planarity : 0.003 0.051 9702 Dihedral : 4.036 57.385 7750 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.73 % Allowed : 34.86 % Favored : 58.41 % 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: 1.71 (0.08), residues: 3976 sheet: -1.59 (0.17), residues: 770 loop : -1.25 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 29 PHE 0.025 0.001 PHE I 225 TYR 0.004 0.001 TYR H 387 ARG 0.007 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 1018 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 625 time to evaluate : 4.741 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: A 31 GLU cc_start: 0.7118 (pm20) cc_final: 0.6851 (pm20) REVERT: A 102 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: A 170 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 271 ARG cc_start: 0.6291 (mmt90) cc_final: 0.5926 (mmt90) REVERT: A 312 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8632 (ptpt) REVERT: A 420 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7745 (tptm) REVERT: A 431 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.7973 (tpp-160) REVERT: B 31 GLU cc_start: 0.7140 (pm20) cc_final: 0.6801 (pm20) REVERT: B 75 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8007 (tp) REVERT: B 88 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8600 (mm) REVERT: B 89 LYS cc_start: 0.8658 (tppt) cc_final: 0.8149 (ttpt) REVERT: B 102 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: B 138 ASN cc_start: 0.8856 (t0) cc_final: 0.8464 (t0) REVERT: B 172 GLN cc_start: 0.8533 (tt0) cc_final: 0.8127 (tp-100) REVERT: B 337 LYS cc_start: 0.8346 (ttmm) cc_final: 0.7853 (mtmt) REVERT: B 373 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6161 (pt0) REVERT: B 407 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8691 (mmmm) REVERT: B 431 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8103 (tpp-160) REVERT: B 484 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8490 (tp30) REVERT: C 88 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8726 (mm) REVERT: C 100 LEU cc_start: 0.8900 (mt) cc_final: 0.8665 (mt) REVERT: C 102 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8019 (mt-10) REVERT: C 431 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.7827 (tpp-160) REVERT: C 537 ASP cc_start: 0.8403 (m-30) cc_final: 0.7754 (m-30) REVERT: D 31 GLU cc_start: 0.7248 (pm20) cc_final: 0.6897 (pm20) REVERT: D 62 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8226 (mmt90) REVERT: D 161 LYS cc_start: 0.7953 (pptt) cc_final: 0.7585 (pptt) REVERT: D 278 GLU cc_start: 0.4949 (OUTLIER) cc_final: 0.3861 (mm-30) REVERT: D 431 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.7917 (mmt180) REVERT: E 31 GLU cc_start: 0.7083 (pm20) cc_final: 0.6774 (pm20) REVERT: E 192 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7797 (ppp) REVERT: E 271 ARG cc_start: 0.6351 (mmt90) cc_final: 0.6042 (mmt90) REVERT: E 337 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8132 (mtpp) REVERT: E 373 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5217 (tp30) REVERT: E 420 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7703 (tptm) REVERT: E 431 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7974 (mmp80) REVERT: F 88 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8630 (mm) REVERT: F 89 LYS cc_start: 0.8647 (tppt) cc_final: 0.8338 (tttt) REVERT: F 138 ASN cc_start: 0.8783 (t0) cc_final: 0.8392 (t0) REVERT: F 170 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8368 (mt) REVERT: F 192 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8478 (ppp) REVERT: F 278 GLU cc_start: 0.4776 (OUTLIER) cc_final: 0.4005 (mm-30) REVERT: F 387 TYR cc_start: 0.2326 (OUTLIER) cc_final: 0.1789 (m-80) REVERT: F 431 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.8071 (tpp80) REVERT: G 31 GLU cc_start: 0.7186 (pm20) cc_final: 0.6803 (pm20) REVERT: G 170 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8028 (mt) REVERT: G 192 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.7771 (ppp) REVERT: G 201 ILE cc_start: 0.8124 (tp) cc_final: 0.7860 (tp) REVERT: G 278 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4610 (mm-30) REVERT: G 337 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8032 (mtmt) REVERT: G 420 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7650 (tptm) REVERT: G 431 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.7935 (mmt180) REVERT: G 537 ASP cc_start: 0.8206 (m-30) cc_final: 0.7565 (m-30) REVERT: H 31 GLU cc_start: 0.7068 (pm20) cc_final: 0.6781 (pm20) REVERT: H 89 LYS cc_start: 0.8781 (tppt) cc_final: 0.8451 (ttpt) REVERT: H 420 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7779 (tptm) REVERT: H 431 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.7965 (tpp-160) REVERT: H 526 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8460 (t0) REVERT: I 31 GLU cc_start: 0.7172 (pm20) cc_final: 0.6871 (pm20) REVERT: I 88 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8616 (mm) REVERT: I 170 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8556 (mt) REVERT: I 278 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4317 (mm-30) REVERT: I 431 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8153 (tpp-160) REVERT: J 88 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8745 (mm) REVERT: J 312 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8236 (ptpt) REVERT: J 431 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7701 (tpp-160) REVERT: J 537 ASP cc_start: 0.8382 (m-30) cc_final: 0.7773 (m-30) REVERT: K 31 GLU cc_start: 0.7269 (pm20) cc_final: 0.6942 (pm20) REVERT: K 102 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8090 (mt-10) REVERT: K 161 LYS cc_start: 0.7706 (pptt) cc_final: 0.7274 (pptt) REVERT: K 192 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8130 (ppp) REVERT: K 278 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.4498 (mm-30) REVERT: K 420 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7956 (tttm) REVERT: L 31 GLU cc_start: 0.7066 (pm20) cc_final: 0.6726 (pm20) REVERT: L 89 LYS cc_start: 0.8649 (tppt) cc_final: 0.7901 (tttp) REVERT: L 138 ASN cc_start: 0.8783 (t0) cc_final: 0.8411 (t0) REVERT: L 192 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8008 (ppp) REVERT: L 271 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6442 (mmt90) REVERT: L 420 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7760 (tptm) REVERT: L 431 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.7986 (tpp-160) REVERT: M 88 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8698 (mm) REVERT: M 89 LYS cc_start: 0.8598 (tppt) cc_final: 0.8206 (tttt) REVERT: M 138 ASN cc_start: 0.8779 (t0) cc_final: 0.8443 (t0) REVERT: M 155 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8259 (tp30) REVERT: M 170 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8487 (mt) REVERT: M 278 GLU cc_start: 0.4766 (OUTLIER) cc_final: 0.3904 (mm-30) REVERT: M 373 GLU cc_start: 0.5001 (OUTLIER) cc_final: 0.4483 (tp30) REVERT: M 387 TYR cc_start: 0.2236 (OUTLIER) cc_final: 0.1655 (m-80) REVERT: M 431 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.7873 (mmt180) REVERT: N 62 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8164 (mtp85) REVERT: N 102 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8089 (mt-10) REVERT: N 138 ASN cc_start: 0.8843 (t0) cc_final: 0.8407 (t0) REVERT: N 278 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4286 (mm-30) REVERT: N 337 LYS cc_start: 0.8261 (ttmm) cc_final: 0.8043 (mtmt) REVERT: N 420 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7954 (tttp) REVERT: N 537 ASP cc_start: 0.8190 (m-30) cc_final: 0.7534 (m-30) outliers start: 393 outliers final: 261 residues processed: 958 average time/residue: 0.5115 time to fit residues: 840.0881 Evaluate side-chains 892 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 588 time to evaluate : 4.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 82 VAL 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 170 ILE 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 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 47 GLU 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 75 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 102 GLU 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 53 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 241 PHE 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 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 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 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 247 LEU 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 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 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 95 LEU 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 333 VAL 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 470 ILE 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 48 THR Chi-restraints excluded: chain F residue 56 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 172 GLN Chi-restraints excluded: chain F residue 192 MET Chi-restraints excluded: chain F residue 200 VAL 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 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 46 VAL 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 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 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 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 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 53 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 69 THR 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 278 GLU Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain I residue 333 VAL 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 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 88 LEU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 260 ILE 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 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 526 ASP 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 48 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 95 LEU 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 254 SER 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 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 36 VAL Chi-restraints excluded: chain L residue 48 THR 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 82 VAL 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 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 411 SER Chi-restraints excluded: chain L residue 420 LYS Chi-restraints excluded: chain L residue 470 ILE Chi-restraints excluded: chain L residue 520 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 82 VAL Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 167 SER 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 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 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 53 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 62 ARG Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 278 GLU 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 416 VAL 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 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: 7.9990 chunk 633 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 413 optimal weight: 5.9990 chunk 173 optimal weight: 30.0000 chunk 704 optimal weight: 10.0000 chunk 584 optimal weight: 1.9990 chunk 326 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 chunk 369 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2315 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= 0.167 Angle : 0.530 9.933 74620 Z= 0.273 Chirality : 0.041 0.257 9086 Planarity : 0.003 0.045 9702 Dihedral : 3.772 56.683 7736 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.86 % Allowed : 36.11 % Favored : 58.03 % 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: 0.49 (0.10), residues: 7364 helix: 1.72 (0.08), residues: 4060 sheet: -1.67 (0.17), residues: 798 loop : -1.32 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 29 PHE 0.024 0.001 PHE I 225 TYR 0.004 0.000 TYR G 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 974 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 632 time to evaluate : 4.726 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 31 GLU cc_start: 0.7155 (pm20) cc_final: 0.6862 (pm20) REVERT: A 102 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: A 312 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8578 (ptpt) REVERT: A 420 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7735 (tptm) REVERT: A 431 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.7960 (tpp-160) REVERT: B 31 GLU cc_start: 0.7216 (pm20) cc_final: 0.6907 (pm20) REVERT: B 88 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8578 (mm) REVERT: B 89 LYS cc_start: 0.8596 (tppt) cc_final: 0.8152 (ttpt) REVERT: B 102 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: B 138 ASN cc_start: 0.8800 (t0) cc_final: 0.8106 (t0) REVERT: B 164 ILE cc_start: 0.7344 (mm) cc_final: 0.7126 (mm) REVERT: B 172 GLN cc_start: 0.8476 (tt0) cc_final: 0.8084 (tp-100) REVERT: B 271 ARG cc_start: 0.6649 (mmt90) cc_final: 0.6407 (mmt90) REVERT: B 337 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7831 (mtmt) REVERT: B 373 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6144 (pt0) REVERT: B 407 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8690 (mmmm) REVERT: B 431 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8106 (tpp-160) REVERT: C 88 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8638 (mm) REVERT: C 100 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8632 (mt) REVERT: C 102 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: C 431 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7826 (tpp-160) REVERT: C 537 ASP cc_start: 0.8417 (m-30) cc_final: 0.7775 (m-30) REVERT: D 31 GLU cc_start: 0.7231 (pm20) cc_final: 0.6875 (pm20) REVERT: D 278 GLU cc_start: 0.5050 (OUTLIER) cc_final: 0.3980 (mm-30) REVERT: D 431 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.7983 (tpp-160) REVERT: E 31 GLU cc_start: 0.7140 (pm20) cc_final: 0.6850 (pm20) REVERT: E 192 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7848 (ppp) REVERT: E 271 ARG cc_start: 0.6518 (mmt90) cc_final: 0.6212 (mmt90) REVERT: E 337 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8083 (mtpp) REVERT: E 420 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7746 (tptm) REVERT: E 431 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.7937 (mmp80) REVERT: F 89 LYS cc_start: 0.8641 (tppt) cc_final: 0.8354 (tttt) REVERT: F 138 ASN cc_start: 0.8715 (t0) cc_final: 0.8341 (t0) REVERT: F 170 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8416 (mt) REVERT: F 192 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8494 (ppp) REVERT: F 278 GLU cc_start: 0.4749 (OUTLIER) cc_final: 0.3971 (mm-30) REVERT: F 326 VAL cc_start: 0.5616 (OUTLIER) cc_final: 0.5334 (m) REVERT: F 387 TYR cc_start: 0.2339 (OUTLIER) cc_final: 0.1812 (m-80) REVERT: F 431 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8110 (tpp80) REVERT: G 31 GLU cc_start: 0.7110 (pm20) cc_final: 0.6725 (pm20) REVERT: G 170 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8018 (mt) REVERT: G 192 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7899 (ppp) REVERT: G 201 ILE cc_start: 0.8120 (tp) cc_final: 0.7842 (tp) REVERT: G 278 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4635 (mm-30) REVERT: G 337 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7910 (mtmt) REVERT: G 420 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7629 (tptm) REVERT: G 431 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.7939 (mmt180) REVERT: G 537 ASP cc_start: 0.8162 (m-30) cc_final: 0.7537 (m-30) REVERT: H 31 GLU cc_start: 0.7051 (pm20) cc_final: 0.6769 (pm20) REVERT: H 89 LYS cc_start: 0.8806 (tppt) cc_final: 0.8493 (ttpt) REVERT: H 420 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7777 (tptm) REVERT: H 431 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.7969 (tpp-160) REVERT: I 31 GLU cc_start: 0.7219 (pm20) cc_final: 0.6899 (pm20) REVERT: I 88 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8545 (mm) REVERT: I 278 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.4579 (mm-30) REVERT: I 431 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8144 (tpp-160) REVERT: J 31 GLU cc_start: 0.7131 (pm20) cc_final: 0.6860 (pm20) REVERT: J 88 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8661 (mm) REVERT: J 102 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: J 192 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8102 (ppp) REVERT: J 312 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8247 (ptpt) REVERT: J 358 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8528 (pt) REVERT: J 431 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7698 (tpp-160) REVERT: J 537 ASP cc_start: 0.8409 (m-30) cc_final: 0.7793 (m-30) REVERT: K 31 GLU cc_start: 0.7217 (pm20) cc_final: 0.6890 (pm20) REVERT: K 102 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8100 (mt-10) REVERT: K 192 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8058 (ppp) REVERT: K 278 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.4484 (mm-30) REVERT: K 431 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.7956 (tpp-160) REVERT: L 31 GLU cc_start: 0.7134 (pm20) cc_final: 0.6823 (pm20) REVERT: L 192 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8033 (ppp) REVERT: L 271 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6542 (mmt90) REVERT: L 420 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7771 (tptm) REVERT: L 431 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8004 (tpp-160) REVERT: M 88 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8659 (mm) REVERT: M 89 LYS cc_start: 0.8592 (tppt) cc_final: 0.8210 (tttt) REVERT: M 138 ASN cc_start: 0.8712 (t0) cc_final: 0.8389 (t0) REVERT: M 155 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8256 (tp30) REVERT: M 278 GLU cc_start: 0.4879 (OUTLIER) cc_final: 0.3983 (mm-30) REVERT: M 373 GLU cc_start: 0.4937 (OUTLIER) cc_final: 0.4443 (tp30) REVERT: M 387 TYR cc_start: 0.2217 (OUTLIER) cc_final: 0.1641 (m-10) REVERT: M 431 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.7950 (tpp-160) REVERT: N 62 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8206 (mtp85) REVERT: N 102 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: N 138 ASN cc_start: 0.8792 (t0) cc_final: 0.8349 (t0) REVERT: N 278 GLU cc_start: 0.5226 (OUTLIER) cc_final: 0.4455 (mm-30) REVERT: N 337 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7996 (mtmt) REVERT: N 420 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7916 (tttp) REVERT: N 537 ASP cc_start: 0.8195 (m-30) cc_final: 0.7539 (m-30) outliers start: 342 outliers final: 233 residues processed: 910 average time/residue: 0.5065 time to fit residues: 792.1053 Evaluate side-chains 879 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 606 time to evaluate : 4.797 ------------------------------------------------------------------------------- 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 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 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 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 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 47 GLU 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 102 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 254 SER 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 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 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 88 LEU 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 150 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 254 SER 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 326 VAL 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 411 SER 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 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 56 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 192 MET Chi-restraints excluded: chain D residue 247 LEU 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 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 36 VAL Chi-restraints excluded: chain E residue 56 THR 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 254 SER 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 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 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 75 ILE 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 192 MET Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 278 GLU 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 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 56 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 95 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 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 530 VAL Chi-restraints excluded: chain G residue 541 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 69 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 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 470 ILE 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 46 VAL Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 254 SER 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 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 67 GLU Chi-restraints excluded: chain J residue 88 LEU 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 254 SER 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 470 ILE Chi-restraints excluded: chain J residue 492 VAL Chi-restraints excluded: chain J residue 530 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 192 MET 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 327 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 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 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 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 530 VAL Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 167 SER 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 427 LEU Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 62 ARG Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 82 VAL Chi-restraints excluded: chain N residue 95 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 278 GLU Chi-restraints excluded: chain N residue 307 PHE 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 470 ILE 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: 2.9990 chunk 79 optimal weight: 30.0000 chunk 401 optimal weight: 30.0000 chunk 514 optimal weight: 0.5980 chunk 398 optimal weight: 7.9990 chunk 592 optimal weight: 0.4980 chunk 393 optimal weight: 10.0000 chunk 701 optimal weight: 50.0000 chunk 439 optimal weight: 9.9990 chunk 427 optimal weight: 5.9990 chunk 323 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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: 0.7726 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 55272 Z= 0.189 Angle : 0.545 10.869 74620 Z= 0.279 Chirality : 0.042 0.249 9086 Planarity : 0.003 0.044 9702 Dihedral : 3.708 51.567 7730 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.98 % Allowed : 36.13 % Favored : 57.90 % 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: 1.72 (0.08), residues: 4060 sheet: -1.53 (0.17), residues: 770 loop : -1.33 (0.11), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 29 PHE 0.023 0.001 PHE I 225 TYR 0.003 0.000 TYR K 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 970 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 621 time to evaluate : 4.748 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 31 GLU cc_start: 0.7159 (pm20) cc_final: 0.6825 (pm20) REVERT: A 102 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: A 271 ARG cc_start: 0.6047 (mmt90) cc_final: 0.5736 (mmt90) REVERT: A 312 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8578 (ptpt) REVERT: A 420 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7701 (tptm) REVERT: A 431 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.7984 (tpp-160) REVERT: B 31 GLU cc_start: 0.7210 (pm20) cc_final: 0.6878 (pm20) REVERT: B 88 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8589 (mm) REVERT: B 89 LYS cc_start: 0.8643 (tppt) cc_final: 0.8160 (ttpt) REVERT: B 102 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: B 138 ASN cc_start: 0.8760 (t0) cc_final: 0.8287 (t0) REVERT: B 172 GLN cc_start: 0.8473 (tt0) cc_final: 0.8074 (tp-100) REVERT: B 337 LYS cc_start: 0.8367 (ttmm) cc_final: 0.7875 (mtmt) REVERT: B 373 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6158 (pt0) REVERT: B 407 LYS cc_start: 0.9243 (mmmt) cc_final: 0.8701 (mmmm) REVERT: B 431 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8120 (tpp-160) REVERT: C 31 GLU cc_start: 0.7156 (pm20) cc_final: 0.6898 (pm20) REVERT: C 88 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8638 (mm) REVERT: C 100 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8592 (mt) REVERT: C 102 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: C 431 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7856 (tpp-160) REVERT: C 537 ASP cc_start: 0.8461 (m-30) cc_final: 0.7819 (m-30) REVERT: D 31 GLU cc_start: 0.7263 (pm20) cc_final: 0.6888 (pm20) REVERT: D 62 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8267 (mmt90) REVERT: D 161 LYS cc_start: 0.7832 (pptt) cc_final: 0.7449 (pptt) REVERT: D 163 ASP cc_start: 0.6938 (t0) cc_final: 0.6658 (t0) REVERT: D 278 GLU cc_start: 0.4953 (OUTLIER) cc_final: 0.3909 (mm-30) REVERT: D 431 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.7979 (tpp-160) REVERT: E 31 GLU cc_start: 0.7153 (pm20) cc_final: 0.6861 (pm20) REVERT: E 192 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7965 (ppp) REVERT: E 271 ARG cc_start: 0.6532 (mmt90) cc_final: 0.6229 (mmt90) REVERT: E 373 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5390 (tp30) REVERT: E 420 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7751 (tptm) REVERT: E 431 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.7980 (mmp80) REVERT: F 89 LYS cc_start: 0.8632 (tppt) cc_final: 0.8382 (tttt) REVERT: F 138 ASN cc_start: 0.8707 (t0) cc_final: 0.8312 (t0) REVERT: F 170 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8473 (mt) REVERT: F 192 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8514 (ppp) REVERT: F 278 GLU cc_start: 0.4688 (OUTLIER) cc_final: 0.3877 (mm-30) REVERT: F 326 VAL cc_start: 0.5627 (OUTLIER) cc_final: 0.5354 (m) REVERT: F 387 TYR cc_start: 0.2231 (OUTLIER) cc_final: 0.1697 (m-80) REVERT: F 431 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8176 (tpp80) REVERT: G 31 GLU cc_start: 0.7121 (pm20) cc_final: 0.6685 (pm20) REVERT: G 170 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8035 (mt) REVERT: G 192 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.7868 (ppp) REVERT: G 271 ARG cc_start: 0.6234 (mmt90) cc_final: 0.6019 (mmt90) REVERT: G 278 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4618 (mm-30) REVERT: G 337 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8114 (mtmt) REVERT: G 431 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.7935 (mmt180) REVERT: G 537 ASP cc_start: 0.8191 (m-30) cc_final: 0.7558 (m-30) REVERT: H 31 GLU cc_start: 0.7088 (pm20) cc_final: 0.6766 (pm20) REVERT: H 89 LYS cc_start: 0.8809 (tppt) cc_final: 0.8510 (ttpt) REVERT: H 420 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7772 (tptm) REVERT: H 431 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.7989 (tpp-160) REVERT: I 31 GLU cc_start: 0.7257 (pm20) cc_final: 0.6973 (pm20) REVERT: I 88 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8558 (mm) REVERT: I 278 GLU cc_start: 0.5534 (OUTLIER) cc_final: 0.4546 (mm-30) REVERT: I 431 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8158 (tpp-160) REVERT: J 31 GLU cc_start: 0.7158 (pm20) cc_final: 0.6829 (pm20) REVERT: J 88 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8682 (mm) REVERT: J 102 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: J 312 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8246 (ptpt) REVERT: J 358 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8581 (pt) REVERT: J 431 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7687 (tpp-160) REVERT: J 537 ASP cc_start: 0.8413 (m-30) cc_final: 0.7804 (m-30) REVERT: K 31 GLU cc_start: 0.7255 (pm20) cc_final: 0.6888 (pm20) REVERT: K 102 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: K 161 LYS cc_start: 0.7792 (pptt) cc_final: 0.7412 (pptt) REVERT: K 192 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8054 (ppp) REVERT: K 278 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.4472 (mm-30) REVERT: K 431 ARG cc_start: 0.8742 (mmm-85) cc_final: 0.7953 (tpp-160) REVERT: L 31 GLU cc_start: 0.7155 (pm20) cc_final: 0.6813 (pm20) REVERT: L 192 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8039 (ppp) REVERT: L 271 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6313 (mmt90) REVERT: L 420 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7763 (tptm) REVERT: L 431 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8014 (tpp-160) REVERT: M 88 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (mm) REVERT: M 89 LYS cc_start: 0.8636 (tppt) cc_final: 0.8240 (tttt) REVERT: M 138 ASN cc_start: 0.8718 (t0) cc_final: 0.8372 (t0) REVERT: M 155 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8250 (tp30) REVERT: M 217 GLU cc_start: 0.6965 (tp30) cc_final: 0.6718 (tp30) REVERT: M 278 GLU cc_start: 0.4740 (OUTLIER) cc_final: 0.3802 (mm-30) REVERT: M 373 GLU cc_start: 0.5000 (OUTLIER) cc_final: 0.4502 (tp30) REVERT: M 387 TYR cc_start: 0.2224 (OUTLIER) cc_final: 0.1641 (m-10) REVERT: M 431 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.7923 (tpp-160) REVERT: N 102 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: N 278 GLU cc_start: 0.5211 (OUTLIER) cc_final: 0.4429 (mm-30) REVERT: N 337 LYS cc_start: 0.8226 (ttmm) cc_final: 0.8005 (mtmt) REVERT: N 420 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7871 (tttp) REVERT: N 537 ASP cc_start: 0.8207 (m-30) cc_final: 0.7552 (m-30) outliers start: 349 outliers final: 265 residues processed: 910 average time/residue: 0.4923 time to fit residues: 771.3962 Evaluate side-chains 901 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 596 time to evaluate : 4.712 ------------------------------------------------------------------------------- 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 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 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 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 47 GLU 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 102 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 254 SER 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 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 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 88 LEU 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 150 VAL Chi-restraints excluded: chain C residue 192 MET 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 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 411 SER Chi-restraints excluded: chain C residue 450 SER 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 36 VAL Chi-restraints excluded: chain D residue 47 GLU 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 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 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 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 36 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 82 VAL 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 254 SER 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 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 69 THR 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 192 MET Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 254 SER Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 278 GLU 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 G residue 46 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 95 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 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 450 SER Chi-restraints excluded: chain G residue 470 ILE 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 56 THR Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 150 VAL 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 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 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 82 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 LEU 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 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 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 88 LEU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 247 LEU 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 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 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 56 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 129 MET 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 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 76 THR Chi-restraints excluded: chain L residue 82 VAL 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 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 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 47 GLU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 67 GLU 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 167 SER 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 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 M residue 541 VAL Chi-restraints excluded: chain N residue 46 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 82 VAL Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 102 GLU 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 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 470 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 30.0000 chunk 280 optimal weight: 3.9990 chunk 419 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 446 optimal weight: 1.9990 chunk 478 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 551 optimal weight: 30.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55272 Z= 0.220 Angle : 0.557 12.162 74620 Z= 0.286 Chirality : 0.042 0.247 9086 Planarity : 0.003 0.043 9702 Dihedral : 3.723 36.531 7730 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 6.73 % Allowed : 35.22 % Favored : 58.05 % 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: 0.46 (0.10), residues: 7364 helix: 1.69 (0.08), residues: 4060 sheet: -1.60 (0.17), residues: 798 loop : -1.34 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 29 PHE 0.022 0.001 PHE I 225 TYR 0.003 0.000 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 1002 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 609 time to evaluate : 4.773 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: A 31 GLU cc_start: 0.7184 (pm20) cc_final: 0.6844 (pm20) REVERT: A 271 ARG cc_start: 0.6094 (mmt90) cc_final: 0.5799 (mmt90) REVERT: A 312 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8606 (ptpt) REVERT: A 420 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7743 (tptm) REVERT: A 431 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.7992 (tpp-160) REVERT: B 31 GLU cc_start: 0.7196 (pm20) cc_final: 0.6864 (pm20) REVERT: B 88 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8611 (mm) REVERT: B 89 LYS cc_start: 0.8667 (tppt) cc_final: 0.8140 (ttmt) REVERT: B 102 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: B 138 ASN cc_start: 0.8780 (t0) cc_final: 0.8247 (t0) REVERT: B 172 GLN cc_start: 0.8492 (tt0) cc_final: 0.8081 (tp-100) REVERT: B 278 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.4702 (mm-30) REVERT: B 337 LYS cc_start: 0.8378 (ttmm) cc_final: 0.7879 (mtmt) REVERT: B 373 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6205 (pt0) REVERT: B 407 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8713 (mmmm) REVERT: B 431 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8155 (tpp-160) REVERT: C 31 GLU cc_start: 0.7186 (pm20) cc_final: 0.6896 (pm20) REVERT: C 88 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8681 (mm) REVERT: C 100 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8683 (mt) REVERT: C 431 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7841 (tpp-160) REVERT: C 537 ASP cc_start: 0.8420 (m-30) cc_final: 0.7784 (m-30) REVERT: D 31 GLU cc_start: 0.7268 (pm20) cc_final: 0.6847 (pm20) REVERT: D 161 LYS cc_start: 0.7907 (pptt) cc_final: 0.7536 (pptt) REVERT: D 163 ASP cc_start: 0.6960 (t0) cc_final: 0.6705 (t0) REVERT: D 278 GLU cc_start: 0.4934 (OUTLIER) cc_final: 0.3866 (mm-30) REVERT: D 431 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8000 (tpp-160) REVERT: E 31 GLU cc_start: 0.7185 (pm20) cc_final: 0.6855 (pm20) REVERT: E 192 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.7940 (ppp) REVERT: E 373 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5372 (tp30) REVERT: E 420 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7757 (tptm) REVERT: E 431 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.7994 (mmp80) REVERT: F 89 LYS cc_start: 0.8657 (tppt) cc_final: 0.8393 (tttt) REVERT: F 138 ASN cc_start: 0.8740 (t0) cc_final: 0.8341 (t0) REVERT: F 170 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8645 (mt) REVERT: F 192 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8507 (ppp) REVERT: F 278 GLU cc_start: 0.4635 (OUTLIER) cc_final: 0.3690 (mm-30) REVERT: F 326 VAL cc_start: 0.5666 (OUTLIER) cc_final: 0.5409 (m) REVERT: F 387 TYR cc_start: 0.2226 (OUTLIER) cc_final: 0.1668 (m-80) REVERT: F 431 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8261 (tpp80) REVERT: G 31 GLU cc_start: 0.7144 (pm20) cc_final: 0.6690 (pm20) REVERT: G 192 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8117 (ppp) REVERT: G 278 GLU cc_start: 0.5253 (OUTLIER) cc_final: 0.4575 (mm-30) REVERT: G 337 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8300 (mtmt) REVERT: G 537 ASP cc_start: 0.8177 (m-30) cc_final: 0.7536 (m-30) REVERT: H 31 GLU cc_start: 0.7109 (pm20) cc_final: 0.6786 (pm20) REVERT: H 89 LYS cc_start: 0.8856 (tppt) cc_final: 0.8525 (ttmt) REVERT: H 373 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5809 (tp30) REVERT: H 420 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7771 (tptm) REVERT: H 431 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.7999 (tpp-160) REVERT: I 31 GLU cc_start: 0.7252 (pm20) cc_final: 0.6940 (pm20) REVERT: I 88 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8572 (mm) REVERT: I 278 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.4533 (mm-30) REVERT: I 431 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.8246 (tpp-160) REVERT: J 31 GLU cc_start: 0.7159 (pm20) cc_final: 0.6841 (pm20) REVERT: J 88 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8720 (mm) REVERT: J 102 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: J 312 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8243 (ptpt) REVERT: J 358 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8550 (pt) REVERT: J 431 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7698 (tpp-160) REVERT: J 537 ASP cc_start: 0.8415 (m-30) cc_final: 0.7807 (m-30) REVERT: K 31 GLU cc_start: 0.7299 (pm20) cc_final: 0.6925 (pm20) REVERT: K 102 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: K 278 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4457 (mm-30) REVERT: K 431 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.7939 (tpp-160) REVERT: L 31 GLU cc_start: 0.7224 (pm20) cc_final: 0.6873 (pm20) REVERT: L 138 ASN cc_start: 0.8722 (t0) cc_final: 0.8479 (t0) REVERT: L 192 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8038 (ppp) REVERT: L 271 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6447 (mmt90) REVERT: L 420 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7766 (tptm) REVERT: L 431 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8017 (tpp-160) REVERT: M 88 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8667 (mm) REVERT: M 89 LYS cc_start: 0.8652 (tppt) cc_final: 0.8344 (tttt) REVERT: M 138 ASN cc_start: 0.8763 (t0) cc_final: 0.8408 (t0) REVERT: M 155 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8248 (tp30) REVERT: M 278 GLU cc_start: 0.4709 (OUTLIER) cc_final: 0.3790 (mm-30) REVERT: M 387 TYR cc_start: 0.2249 (OUTLIER) cc_final: 0.1646 (m-10) REVERT: M 431 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8249 (tpp80) REVERT: N 29 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6122 (t-170) REVERT: N 100 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8647 (mt) REVERT: N 102 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: N 271 ARG cc_start: 0.6196 (mmt90) cc_final: 0.5993 (mmt90) REVERT: N 278 GLU cc_start: 0.5191 (OUTLIER) cc_final: 0.4404 (mm-30) REVERT: N 337 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7953 (mtmt) REVERT: N 420 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7816 (tttp) REVERT: N 537 ASP cc_start: 0.8216 (m-30) cc_final: 0.7565 (m-30) outliers start: 393 outliers final: 311 residues processed: 937 average time/residue: 0.4944 time to fit residues: 801.7560 Evaluate side-chains 948 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 599 time to evaluate : 4.769 ------------------------------------------------------------------------------- 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 67 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 82 VAL 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 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 47 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 274 VAL 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 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 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 67 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 VAL 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 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 411 SER Chi-restraints excluded: chain C residue 450 SER 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 536 ILE 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 56 THR 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 254 SER 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 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 36 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 82 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 254 SER 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 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 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 69 THR Chi-restraints excluded: chain F residue 82 VAL 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 192 MET 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 260 ILE Chi-restraints excluded: chain F residue 278 GLU 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 G residue 46 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 56 THR 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 102 GLU Chi-restraints excluded: chain G residue 150 VAL 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 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 411 SER Chi-restraints excluded: chain G residue 435 GLU 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 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 56 THR Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 150 VAL 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 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 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 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 82 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 LEU 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 I residue 541 VAL Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 150 VAL 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 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 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 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 247 LEU 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 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 76 THR Chi-restraints excluded: chain L residue 82 VAL 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 254 SER 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 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 520 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 56 THR Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 82 VAL 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 167 SER 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 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 N residue 29 HIS Chi-restraints excluded: chain N residue 46 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 69 THR Chi-restraints excluded: chain N residue 82 VAL 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 150 VAL Chi-restraints excluded: chain N residue 246 ILE 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 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 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: 5.9990 chunk 672 optimal weight: 9.9990 chunk 613 optimal weight: 4.9990 chunk 653 optimal weight: 9.9990 chunk 393 optimal weight: 9.9990 chunk 284 optimal weight: 0.6980 chunk 513 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 590 optimal weight: 2.9990 chunk 618 optimal weight: 5.9990 chunk 651 optimal weight: 30.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55272 Z= 0.209 Angle : 0.557 11.985 74620 Z= 0.287 Chirality : 0.042 0.251 9086 Planarity : 0.003 0.043 9702 Dihedral : 3.711 17.580 7730 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.51 % Allowed : 35.58 % Favored : 57.91 % 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: 0.54 (0.10), residues: 7364 helix: 1.78 (0.08), residues: 3976 sheet: -1.55 (0.17), residues: 798 loop : -1.27 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 29 PHE 0.020 0.001 PHE I 225 TYR 0.003 0.000 TYR J 387 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 995 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 615 time to evaluate : 4.793 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: 0.7176 (pm20) cc_final: 0.6831 (pm20) REVERT: A 89 LYS cc_start: 0.8779 (tppt) cc_final: 0.8057 (tttt) REVERT: A 102 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: A 271 ARG cc_start: 0.6042 (mmt90) cc_final: 0.5760 (mmt90) REVERT: A 312 LYS cc_start: 0.8936 (mmtm) cc_final: 0.8573 (ptpt) REVERT: A 420 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7736 (tptm) REVERT: A 431 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.7990 (tpp-160) REVERT: B 31 GLU cc_start: 0.7090 (pm20) cc_final: 0.6770 (pm20) REVERT: B 88 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8633 (mm) REVERT: B 89 LYS cc_start: 0.8665 (tppt) cc_final: 0.8144 (ttmt) REVERT: B 102 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: B 138 ASN cc_start: 0.8774 (t0) cc_final: 0.8301 (t0) REVERT: B 172 GLN cc_start: 0.8490 (tt0) cc_final: 0.8078 (tp-100) REVERT: B 278 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.4669 (mm-30) REVERT: B 337 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7899 (mtmt) REVERT: B 373 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6197 (pt0) REVERT: B 407 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8704 (mmmm) REVERT: B 431 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8176 (tpp-160) REVERT: C 31 GLU cc_start: 0.7196 (pm20) cc_final: 0.6903 (pm20) REVERT: C 88 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8680 (mm) REVERT: C 100 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8679 (mt) REVERT: C 431 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7840 (tpp-160) REVERT: C 537 ASP cc_start: 0.8430 (m-30) cc_final: 0.7796 (m-30) REVERT: D 31 GLU cc_start: 0.7325 (pm20) cc_final: 0.6899 (pm20) REVERT: D 161 LYS cc_start: 0.7875 (pptt) cc_final: 0.7506 (pptt) REVERT: D 163 ASP cc_start: 0.7065 (t0) cc_final: 0.6793 (t0) REVERT: D 278 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.3864 (mm-30) REVERT: D 431 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8011 (tpp-160) REVERT: E 31 GLU cc_start: 0.7216 (pm20) cc_final: 0.6885 (pm20) REVERT: E 192 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.7934 (ppp) REVERT: E 373 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5373 (tp30) REVERT: E 420 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7730 (tptm) REVERT: E 431 ARG cc_start: 0.8551 (mmm-85) cc_final: 0.8019 (mmp80) REVERT: F 89 LYS cc_start: 0.8656 (tppt) cc_final: 0.8398 (tttt) REVERT: F 138 ASN cc_start: 0.8742 (t0) cc_final: 0.8346 (t0) REVERT: F 192 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8564 (ppp) REVERT: F 252 LYS cc_start: 0.8463 (ttmt) cc_final: 0.7968 (mmmm) REVERT: F 278 GLU cc_start: 0.4447 (OUTLIER) cc_final: 0.3340 (mm-30) REVERT: F 326 VAL cc_start: 0.5651 (OUTLIER) cc_final: 0.5409 (m) REVERT: F 387 TYR cc_start: 0.2013 (OUTLIER) cc_final: 0.1477 (m-80) REVERT: F 431 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8264 (tpp80) REVERT: G 31 GLU cc_start: 0.7152 (pm20) cc_final: 0.6692 (pm20) REVERT: G 100 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8688 (mt) REVERT: G 192 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8043 (ppp) REVERT: G 278 GLU cc_start: 0.5226 (OUTLIER) cc_final: 0.4539 (mm-30) REVERT: G 431 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.7905 (tpp-160) REVERT: G 537 ASP cc_start: 0.8178 (m-30) cc_final: 0.7534 (m-30) REVERT: H 31 GLU cc_start: 0.7084 (pm20) cc_final: 0.6754 (pm20) REVERT: H 89 LYS cc_start: 0.8820 (tppt) cc_final: 0.8523 (ttmt) REVERT: H 373 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5800 (tp30) REVERT: H 420 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7782 (tptm) REVERT: H 431 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8002 (tpp-160) REVERT: I 31 GLU cc_start: 0.7265 (pm20) cc_final: 0.6958 (pm20) REVERT: I 88 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8569 (mm) REVERT: I 278 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4507 (mm-30) REVERT: I 431 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8232 (tpp-160) REVERT: J 31 GLU cc_start: 0.7152 (pm20) cc_final: 0.6809 (pm20) REVERT: J 88 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8718 (mm) REVERT: J 102 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: J 312 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8242 (ptpt) REVERT: J 358 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8561 (pt) REVERT: J 431 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7695 (tpp-160) REVERT: J 537 ASP cc_start: 0.8422 (m-30) cc_final: 0.7815 (m-30) REVERT: K 31 GLU cc_start: 0.7363 (pm20) cc_final: 0.6985 (pm20) REVERT: K 102 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: K 278 GLU cc_start: 0.5425 (OUTLIER) cc_final: 0.4438 (mm-30) REVERT: K 431 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.7936 (tpp-160) REVERT: L 31 GLU cc_start: 0.7255 (pm20) cc_final: 0.6912 (pm20) REVERT: L 138 ASN cc_start: 0.8782 (t0) cc_final: 0.8460 (t0) REVERT: L 192 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8118 (ppp) REVERT: L 271 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6378 (mmt90) REVERT: L 420 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7738 (tptm) REVERT: L 431 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.8034 (tpp-160) REVERT: M 88 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8645 (mm) REVERT: M 89 LYS cc_start: 0.8645 (tppt) cc_final: 0.8337 (tttt) REVERT: M 138 ASN cc_start: 0.8757 (t0) cc_final: 0.8413 (t0) REVERT: M 155 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8252 (tp30) REVERT: M 278 GLU cc_start: 0.4680 (OUTLIER) cc_final: 0.3757 (mm-30) REVERT: M 387 TYR cc_start: 0.2151 (OUTLIER) cc_final: 0.1563 (m-10) REVERT: M 431 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.7927 (tpp-160) REVERT: N 29 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.6168 (t-170) REVERT: N 100 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8637 (mt) REVERT: N 102 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: N 271 ARG cc_start: 0.6112 (mmt90) cc_final: 0.5886 (mmt90) REVERT: N 278 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4329 (mm-30) REVERT: N 337 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7966 (mtmt) REVERT: N 354 GLU cc_start: 0.8158 (mp0) cc_final: 0.7939 (mp0) REVERT: N 420 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7618 (tptm) REVERT: N 537 ASP cc_start: 0.8216 (m-30) cc_final: 0.7559 (m-30) outliers start: 380 outliers final: 310 residues processed: 931 average time/residue: 0.4861 time to fit residues: 781.8615 Evaluate side-chains 953 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 604 time to evaluate : 4.732 ------------------------------------------------------------------------------- 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 67 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 82 VAL 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 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 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 47 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 274 VAL 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 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 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 VAL 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 450 SER 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 536 ILE 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 56 THR Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 82 VAL 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 254 SER 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 349 ILE Chi-restraints excluded: chain D residue 387 TYR Chi-restraints excluded: chain D residue 406 ILE 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 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 36 VAL Chi-restraints excluded: chain E residue 47 GLU 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 82 VAL 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 254 SER 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 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 95 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 192 MET 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 260 ILE Chi-restraints excluded: chain F residue 278 GLU 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 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 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 192 MET 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 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 470 ILE 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 56 THR Chi-restraints excluded: chain H residue 67 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 129 MET 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 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 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 82 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 95 LEU 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 47 GLU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 247 LEU 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 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 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 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 200 VAL 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 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 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 69 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 82 VAL 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 254 SER 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 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 520 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 48 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 82 VAL 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 167 SER 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 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 450 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 29 HIS Chi-restraints excluded: chain N residue 46 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 82 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 246 ILE 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 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 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: 8.9990 chunk 691 optimal weight: 10.0000 chunk 422 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 480 optimal weight: 1.9990 chunk 725 optimal weight: 9.9990 chunk 667 optimal weight: 5.9990 chunk 577 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 446 optimal weight: 8.9990 chunk 354 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.7717 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55272 Z= 0.176 Angle : 0.556 12.323 74620 Z= 0.285 Chirality : 0.042 0.304 9086 Planarity : 0.003 0.040 9702 Dihedral : 3.669 17.800 7728 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.50 % Allowed : 36.55 % Favored : 57.95 % 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: 0.59 (0.10), residues: 7364 helix: 1.83 (0.08), residues: 3976 sheet: -1.50 (0.17), residues: 798 loop : -1.26 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 29 PHE 0.028 0.001 PHE N 225 TYR 0.003 0.000 TYR A 387 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 948 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 627 time to evaluate : 4.799 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: A 31 GLU cc_start: 0.7042 (pm20) cc_final: 0.6745 (pm20) REVERT: A 102 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: A 269 MET cc_start: 0.5466 (mtm) cc_final: 0.5012 (ptt) REVERT: A 271 ARG cc_start: 0.6045 (mmt90) cc_final: 0.5661 (mmt90) REVERT: A 312 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8579 (ptpt) REVERT: A 420 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7752 (tptm) REVERT: A 431 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.7957 (tpp-160) REVERT: B 31 GLU cc_start: 0.7084 (pm20) cc_final: 0.6762 (pm20) REVERT: B 88 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8608 (mm) REVERT: B 89 LYS cc_start: 0.8604 (tppt) cc_final: 0.8144 (ttmt) REVERT: B 102 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: B 138 ASN cc_start: 0.8748 (t0) cc_final: 0.8228 (t0) REVERT: B 172 GLN cc_start: 0.8488 (tt0) cc_final: 0.8044 (tp-100) REVERT: B 278 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.4699 (mm-30) REVERT: B 337 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7931 (mtmt) REVERT: B 373 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6176 (pt0) REVERT: B 407 LYS cc_start: 0.9241 (mmmt) cc_final: 0.8716 (mmmm) REVERT: B 431 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8166 (tpp-160) REVERT: C 31 GLU cc_start: 0.7179 (pm20) cc_final: 0.6919 (pm20) REVERT: C 88 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8588 (mm) REVERT: C 100 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8648 (mt) REVERT: C 431 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7825 (tpp-160) REVERT: C 537 ASP cc_start: 0.8471 (m-30) cc_final: 0.7844 (m-30) REVERT: D 31 GLU cc_start: 0.7346 (pm20) cc_final: 0.6960 (pm20) REVERT: D 102 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: D 161 LYS cc_start: 0.7885 (pptt) cc_final: 0.7468 (pptt) REVERT: D 163 ASP cc_start: 0.7073 (t0) cc_final: 0.6755 (t0) REVERT: D 278 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.3840 (mm-30) REVERT: D 431 ARG cc_start: 0.8551 (mmm-85) cc_final: 0.7982 (tpp-160) REVERT: D 481 MET cc_start: 0.8820 (mmt) cc_final: 0.8590 (mmt) REVERT: E 31 GLU cc_start: 0.7214 (pm20) cc_final: 0.6929 (pm20) REVERT: E 192 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.7940 (ppp) REVERT: E 271 ARG cc_start: 0.6222 (mmt90) cc_final: 0.6021 (mpt-90) REVERT: E 373 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5375 (tp30) REVERT: E 420 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7731 (tptm) REVERT: E 431 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8015 (mmp80) REVERT: F 89 LYS cc_start: 0.8656 (tppt) cc_final: 0.8388 (tttt) REVERT: F 138 ASN cc_start: 0.8703 (t0) cc_final: 0.8311 (t0) REVERT: F 192 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8574 (ppp) REVERT: F 252 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8112 (tptp) REVERT: F 278 GLU cc_start: 0.4345 (OUTLIER) cc_final: 0.2868 (mm-30) REVERT: F 326 VAL cc_start: 0.5634 (OUTLIER) cc_final: 0.5396 (m) REVERT: F 387 TYR cc_start: 0.1999 (OUTLIER) cc_final: 0.1470 (m-80) REVERT: F 431 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8266 (tpp80) REVERT: G 31 GLU cc_start: 0.7146 (pm20) cc_final: 0.6682 (pm20) REVERT: G 100 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8712 (mt) REVERT: G 192 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8042 (ppp) REVERT: G 278 GLU cc_start: 0.5269 (OUTLIER) cc_final: 0.4533 (mm-30) REVERT: G 431 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.7885 (tpp-160) REVERT: G 537 ASP cc_start: 0.8204 (m-30) cc_final: 0.7574 (m-30) REVERT: H 31 GLU cc_start: 0.6982 (pm20) cc_final: 0.6681 (pm20) REVERT: H 89 LYS cc_start: 0.8840 (tppt) cc_final: 0.8525 (ttmt) REVERT: H 155 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8179 (mm-30) REVERT: H 373 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5806 (tp30) REVERT: H 420 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7675 (tptm) REVERT: H 431 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8000 (tpp-160) REVERT: I 31 GLU cc_start: 0.7249 (pm20) cc_final: 0.6974 (pm20) REVERT: I 88 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8576 (mm) REVERT: I 278 GLU cc_start: 0.5472 (OUTLIER) cc_final: 0.4465 (mm-30) REVERT: I 431 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.8233 (tpp-160) REVERT: J 31 GLU cc_start: 0.7105 (pm20) cc_final: 0.6805 (pm20) REVERT: J 88 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8640 (mm) REVERT: J 431 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7664 (tpp-160) REVERT: J 537 ASP cc_start: 0.8449 (m-30) cc_final: 0.7862 (m-30) REVERT: K 31 GLU cc_start: 0.7356 (pm20) cc_final: 0.7031 (pm20) REVERT: K 102 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: K 161 LYS cc_start: 0.7748 (pptt) cc_final: 0.7311 (pptt) REVERT: K 163 ASP cc_start: 0.7062 (t0) cc_final: 0.6705 (t0) REVERT: K 278 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.4583 (mm-30) REVERT: K 431 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.7913 (tpp-160) REVERT: L 31 GLU cc_start: 0.7118 (pm20) cc_final: 0.6801 (pm20) REVERT: L 138 ASN cc_start: 0.8729 (t0) cc_final: 0.8428 (t0) REVERT: L 192 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8137 (ppp) REVERT: L 271 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6469 (mmt90) REVERT: L 420 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7773 (tptm) REVERT: L 431 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8033 (tpp-160) REVERT: M 89 LYS cc_start: 0.8636 (tppt) cc_final: 0.8262 (tttt) REVERT: M 138 ASN cc_start: 0.8769 (t0) cc_final: 0.8392 (t0) REVERT: M 155 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8240 (tp30) REVERT: M 278 GLU cc_start: 0.4654 (OUTLIER) cc_final: 0.3714 (mm-30) REVERT: M 387 TYR cc_start: 0.2138 (OUTLIER) cc_final: 0.1555 (m-10) REVERT: M 431 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.7874 (tpp-160) REVERT: N 100 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8660 (mt) REVERT: N 102 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: N 271 ARG cc_start: 0.6125 (mmt90) cc_final: 0.5913 (mmt90) REVERT: N 278 GLU cc_start: 0.5195 (OUTLIER) cc_final: 0.4403 (mm-30) REVERT: N 337 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7781 (mtmt) REVERT: N 354 GLU cc_start: 0.8134 (mp0) cc_final: 0.7920 (mp0) REVERT: N 420 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7602 (tptm) REVERT: N 537 ASP cc_start: 0.8216 (m-30) cc_final: 0.7552 (m-30) outliers start: 321 outliers final: 269 residues processed: 888 average time/residue: 0.4924 time to fit residues: 754.4323 Evaluate side-chains 918 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 613 time to evaluate : 4.776 ------------------------------------------------------------------------------- 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 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 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 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 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 47 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 274 VAL 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 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 492 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 254 SER 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 384 THR Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 450 SER 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 47 GLU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 67 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 81 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 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 406 ILE 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 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 36 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 56 THR 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 254 SER 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 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 95 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 192 MET 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 278 GLU 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 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 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 150 VAL Chi-restraints excluded: chain G residue 192 MET 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 333 VAL 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 470 ILE 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 56 THR 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 150 VAL Chi-restraints excluded: chain H residue 192 MET 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 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 88 LEU Chi-restraints excluded: chain I residue 95 LEU 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 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 88 LEU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 247 LEU 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 333 VAL 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 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 56 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 200 VAL Chi-restraints excluded: chain K residue 247 LEU 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 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 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 76 THR 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 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 56 THR Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 167 SER 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 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 450 SER Chi-restraints excluded: chain M residue 530 VAL Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain N residue 46 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 102 GLU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 246 ILE 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 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 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: 0.3980 chunk 615 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 532 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 578 optimal weight: 0.0470 chunk 242 optimal weight: 6.9990 chunk 593 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 464 GLN M 464 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.197827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141710 restraints weight = 88372.791| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 4.35 r_work: 0.3519 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 55272 Z= 0.150 Angle : 0.555 15.703 74620 Z= 0.282 Chirality : 0.042 0.309 9086 Planarity : 0.003 0.036 9702 Dihedral : 3.598 18.125 7728 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.52 % Allowed : 37.67 % Favored : 57.81 % 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: 0.64 (0.10), residues: 7364 helix: 1.87 (0.08), residues: 3976 sheet: -1.40 (0.17), residues: 798 loop : -1.26 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 267 PHE 0.021 0.001 PHE N 225 TYR 0.004 0.000 TYR J 156 ARG 0.006 0.000 ARG E 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13132.85 seconds wall clock time: 235 minutes 52.13 seconds (14152.13 seconds total)