Starting phenix.real_space_refine on Wed Sep 25 13:16:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/09_2024/8s32_19687.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/09_2024/8s32_19687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/09_2024/8s32_19687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/09_2024/8s32_19687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/09_2024/8s32_19687.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/09_2024/8s32_19687.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.026 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 294 5.16 5 C 34636 2.51 5 N 9562 2.21 5 O 11060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 55552 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3864 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "1" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Restraints were copied for chains: 2, O, Q, P, S, R, U, T, W, V, Y, X, Z, C, B, E, D, G, F, I, H, K, J, M, L, N Time building chain proxies: 11.10, per 1000 atoms: 0.20 Number of scatterers: 55552 At special positions: 0 Unit cell: (155.767, 155.767, 159.294, 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 294 16.00 O 11060 8.00 N 9562 7.00 C 34636 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: 10.61 Conformation dependent library (CDL) restraints added in 5.6 seconds 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13608 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 98 sheets defined 58.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 109 Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 337 through 354 Processing helix chain 'A' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 432 through 446 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 496 through 515 Processing helix chain 'B' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 109 Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.699A pdb=" N MET B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.621A pdb=" N LEU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 337 through 354 Processing helix chain 'B' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 432 through 446 Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 496 through 515 Processing helix chain 'C' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 109 Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.699A pdb=" N MET C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Proline residue: C 234 - end of helix Processing helix chain 'C' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 409 Processing helix chain 'C' and resid 415 through 425 Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 460 through 471 Processing helix chain 'C' and resid 496 through 515 Processing helix chain 'D' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.621A pdb=" N GLU D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 109 Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE D 203 " --> pdb=" O SER D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Proline residue: D 234 - end of helix Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'D' and resid 337 through 354 Processing helix chain 'D' and resid 357 through 374 removed outlier: 4.313A pdb=" N GLY D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 409 Processing helix chain 'D' and resid 415 through 425 Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'D' and resid 496 through 515 Processing helix chain 'E' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 85 removed outlier: 3.594A pdb=" N VAL E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 109 Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 311 Processing helix chain 'E' and resid 337 through 354 Processing helix chain 'E' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY E 374 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 409 Processing helix chain 'E' and resid 415 through 425 Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 447 through 458 Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'E' and resid 496 through 515 Processing helix chain 'F' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 109 Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'F' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY F 158 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.826A pdb=" N PHE F 203 " --> pdb=" O SER F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET F 232 " --> pdb=" O ASN F 228 " (cutoff:3.500A) Proline residue: F 234 - end of helix Processing helix chain 'F' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 311 Processing helix chain 'F' and resid 337 through 354 Processing helix chain 'F' and resid 357 through 374 removed outlier: 4.313A pdb=" N GLY F 374 " --> pdb=" O LYS F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 409 Processing helix chain 'F' and resid 415 through 425 Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 447 through 458 Processing helix chain 'F' and resid 460 through 471 Processing helix chain 'F' and resid 496 through 515 Processing helix chain 'G' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU G 58 " --> pdb=" O SER G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL G 76 " --> pdb=" O MET G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 109 Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE G 203 " --> pdb=" O SER G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) Proline residue: G 234 - end of helix Processing helix chain 'G' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS G 285 " --> pdb=" O GLY G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 311 Processing helix chain 'G' and resid 337 through 354 Processing helix chain 'G' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY G 374 " --> pdb=" O LYS G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 409 Processing helix chain 'G' and resid 415 through 425 Processing helix chain 'G' and resid 432 through 446 Processing helix chain 'G' and resid 447 through 458 Processing helix chain 'G' and resid 460 through 471 Processing helix chain 'G' and resid 496 through 515 Processing helix chain 'H' and resid 8 through 28 removed outlier: 4.224A pdb=" N VAL H 28 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 85 removed outlier: 3.596A pdb=" N VAL H 76 " --> pdb=" O MET H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 109 Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 139 through 151 Processing helix chain 'H' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY H 158 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE H 203 " --> pdb=" O SER H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET H 232 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Proline residue: H 234 - end of helix Processing helix chain 'H' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU H 261 " --> pdb=" O ALA H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS H 285 " --> pdb=" O GLY H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 311 Processing helix chain 'H' and resid 337 through 354 Processing helix chain 'H' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY H 374 " --> pdb=" O LYS H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 409 Processing helix chain 'H' and resid 415 through 425 Processing helix chain 'H' and resid 432 through 446 Processing helix chain 'H' and resid 447 through 458 Processing helix chain 'H' and resid 460 through 471 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'I' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL I 28 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU I 58 " --> pdb=" O SER I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 109 Processing helix chain 'I' and resid 111 through 134 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY I 158 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE I 203 " --> pdb=" O SER I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET I 232 " --> pdb=" O ASN I 228 " (cutoff:3.500A) Proline residue: I 234 - end of helix Processing helix chain 'I' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS I 285 " --> pdb=" O GLY I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 311 Processing helix chain 'I' and resid 337 through 354 Processing helix chain 'I' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY I 374 " --> pdb=" O LYS I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 409 Processing helix chain 'I' and resid 415 through 425 Processing helix chain 'I' and resid 432 through 446 Processing helix chain 'I' and resid 447 through 458 Processing helix chain 'I' and resid 460 through 471 Processing helix chain 'I' and resid 496 through 515 Processing helix chain 'J' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL J 28 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 59 removed outlier: 3.621A pdb=" N GLU J 58 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL J 76 " --> pdb=" O MET J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 109 Processing helix chain 'J' and resid 111 through 134 Processing helix chain 'J' and resid 139 through 151 Processing helix chain 'J' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY J 158 " --> pdb=" O ASP J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE J 203 " --> pdb=" O SER J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET J 232 " --> pdb=" O ASN J 228 " (cutoff:3.500A) Proline residue: J 234 - end of helix Processing helix chain 'J' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU J 261 " --> pdb=" O ALA J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS J 285 " --> pdb=" O GLY J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 311 Processing helix chain 'J' and resid 337 through 354 Processing helix chain 'J' and resid 357 through 374 removed outlier: 4.313A pdb=" N GLY J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 409 Processing helix chain 'J' and resid 415 through 425 Processing helix chain 'J' and resid 432 through 446 Processing helix chain 'J' and resid 447 through 458 Processing helix chain 'J' and resid 460 through 471 Processing helix chain 'J' and resid 496 through 515 Processing helix chain 'K' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL K 76 " --> pdb=" O MET K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 109 Processing helix chain 'K' and resid 111 through 134 Processing helix chain 'K' and resid 139 through 151 Processing helix chain 'K' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY K 158 " --> pdb=" O ASP K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE K 203 " --> pdb=" O SER K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 242 removed outlier: 3.699A pdb=" N MET K 232 " --> pdb=" O ASN K 228 " (cutoff:3.500A) Proline residue: K 234 - end of helix Processing helix chain 'K' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU K 261 " --> pdb=" O ALA K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 296 removed outlier: 3.661A pdb=" N LYS K 285 " --> pdb=" O GLY K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 311 Processing helix chain 'K' and resid 337 through 354 Processing helix chain 'K' and resid 357 through 374 removed outlier: 4.313A pdb=" N GLY K 374 " --> pdb=" O LYS K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 409 Processing helix chain 'K' and resid 415 through 425 Processing helix chain 'K' and resid 432 through 446 Processing helix chain 'K' and resid 447 through 458 Processing helix chain 'K' and resid 460 through 471 Processing helix chain 'K' and resid 496 through 515 Processing helix chain 'L' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL L 28 " --> pdb=" O ASP L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU L 58 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL L 76 " --> pdb=" O MET L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 109 Processing helix chain 'L' and resid 111 through 134 Processing helix chain 'L' and resid 139 through 151 Processing helix chain 'L' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY L 158 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE L 203 " --> pdb=" O SER L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET L 232 " --> pdb=" O ASN L 228 " (cutoff:3.500A) Proline residue: L 234 - end of helix Processing helix chain 'L' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU L 261 " --> pdb=" O ALA L 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS L 285 " --> pdb=" O GLY L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 311 Processing helix chain 'L' and resid 337 through 354 Processing helix chain 'L' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY L 374 " --> pdb=" O LYS L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 409 Processing helix chain 'L' and resid 415 through 425 Processing helix chain 'L' and resid 432 through 446 Processing helix chain 'L' and resid 447 through 458 Processing helix chain 'L' and resid 460 through 471 Processing helix chain 'L' and resid 496 through 515 Processing helix chain 'M' and resid 8 through 28 removed outlier: 4.225A pdb=" N VAL M 28 " --> pdb=" O ASP M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 59 removed outlier: 3.620A pdb=" N GLU M 58 " --> pdb=" O SER M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL M 76 " --> pdb=" O MET M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 109 Processing helix chain 'M' and resid 111 through 134 Processing helix chain 'M' and resid 139 through 151 Processing helix chain 'M' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY M 158 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 204 removed outlier: 3.826A pdb=" N PHE M 203 " --> pdb=" O SER M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET M 232 " --> pdb=" O ASN M 228 " (cutoff:3.500A) Proline residue: M 234 - end of helix Processing helix chain 'M' and resid 257 through 268 removed outlier: 3.620A pdb=" N LEU M 261 " --> pdb=" O ALA M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS M 285 " --> pdb=" O GLY M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 311 Processing helix chain 'M' and resid 337 through 354 Processing helix chain 'M' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY M 374 " --> pdb=" O LYS M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 384 through 409 Processing helix chain 'M' and resid 415 through 425 Processing helix chain 'M' and resid 432 through 446 Processing helix chain 'M' and resid 447 through 458 Processing helix chain 'M' and resid 460 through 471 Processing helix chain 'M' and resid 496 through 515 Processing helix chain 'N' and resid 8 through 28 removed outlier: 4.226A pdb=" N VAL N 28 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 59 removed outlier: 3.621A pdb=" N GLU N 58 " --> pdb=" O SER N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 85 removed outlier: 3.595A pdb=" N VAL N 76 " --> pdb=" O MET N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 109 Processing helix chain 'N' and resid 111 through 134 Processing helix chain 'N' and resid 139 through 151 Processing helix chain 'N' and resid 154 through 169 removed outlier: 3.644A pdb=" N GLY N 158 " --> pdb=" O ASP N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 204 removed outlier: 3.825A pdb=" N PHE N 203 " --> pdb=" O SER N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 242 removed outlier: 3.700A pdb=" N MET N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) Proline residue: N 234 - end of helix Processing helix chain 'N' and resid 257 through 268 removed outlier: 3.621A pdb=" N LEU N 261 " --> pdb=" O ALA N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 281 through 296 removed outlier: 3.660A pdb=" N LYS N 285 " --> pdb=" O GLY N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 311 Processing helix chain 'N' and resid 337 through 354 Processing helix chain 'N' and resid 357 through 374 removed outlier: 4.312A pdb=" N GLY N 374 " --> pdb=" O LYS N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 384 through 409 Processing helix chain 'N' and resid 415 through 425 Processing helix chain 'N' and resid 432 through 446 Processing helix chain 'N' and resid 447 through 458 Processing helix chain 'N' and resid 460 through 471 Processing helix chain 'N' and resid 496 through 515 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 7.549A pdb=" N VAL G 38 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET A 519 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 7.552A pdb=" N ASN A 36 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N MET B 519 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 38 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR B 521 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY A 334 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY A 334 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 218 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 249 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 220 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 246 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL A 275 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE A 248 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 49 removed outlier: 7.550A pdb=" N ASN B 36 " --> pdb=" O GLU C 517 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N MET C 519 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 38 " --> pdb=" O MET C 519 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N THR C 521 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY B 334 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY B 334 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 218 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 249 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 220 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 246 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B 275 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE B 248 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 49 removed outlier: 7.548A pdb=" N ASN C 36 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET D 519 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 38 " --> pdb=" O MET D 519 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR D 521 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 178 Processing sheet with id=AB7, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY C 334 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY C 334 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE C 218 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE C 249 " --> pdb=" O PHE C 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 220 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 246 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL C 275 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 248 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AC2, first strand: chain 'D' and resid 47 through 49 removed outlier: 7.549A pdb=" N ASN D 36 " --> pdb=" O GLU E 517 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET E 519 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL D 38 " --> pdb=" O MET E 519 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR E 521 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 173 through 178 Processing sheet with id=AC4, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY D 334 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY D 334 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE D 218 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 249 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU D 220 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU D 246 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 275 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE D 248 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC7, first strand: chain 'D' and resid 475 through 478 Processing sheet with id=AC8, first strand: chain 'E' and resid 47 through 49 removed outlier: 7.535A pdb=" N ASN E 36 " --> pdb=" O GLU F 517 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET F 519 " --> pdb=" O ASN E 36 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 38 " --> pdb=" O MET F 519 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR F 521 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 173 through 178 Processing sheet with id=AD1, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY E 334 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY E 334 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE E 218 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE E 249 " --> pdb=" O PHE E 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU E 220 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU E 246 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL E 275 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE E 248 " --> pdb=" O VAL E 275 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AD4, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AD5, first strand: chain 'F' and resid 47 through 49 removed outlier: 7.548A pdb=" N ASN F 36 " --> pdb=" O GLU G 517 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET G 519 " --> pdb=" O ASN F 36 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL F 38 " --> pdb=" O MET G 519 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR G 521 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 173 through 178 Processing sheet with id=AD7, first strand: chain 'F' and resid 192 through 194 removed outlier: 6.148A pdb=" N GLY F 334 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 192 through 194 removed outlier: 6.148A pdb=" N GLY F 334 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE F 218 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE F 249 " --> pdb=" O PHE F 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU F 220 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU F 246 " --> pdb=" O ALA F 273 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL F 275 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE F 248 " --> pdb=" O VAL F 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AE1, first strand: chain 'F' and resid 475 through 478 Processing sheet with id=AE2, first strand: chain 'G' and resid 173 through 178 Processing sheet with id=AE3, first strand: chain 'G' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY G 334 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY G 334 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE G 218 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE G 249 " --> pdb=" O PHE G 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU G 220 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU G 246 " --> pdb=" O ALA G 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL G 275 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE G 248 " --> pdb=" O VAL G 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AE6, first strand: chain 'G' and resid 475 through 478 Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 removed outlier: 7.554A pdb=" N VAL N 38 " --> pdb=" O GLU H 517 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET H 519 " --> pdb=" O VAL N 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 47 through 49 removed outlier: 7.549A pdb=" N ASN H 36 " --> pdb=" O GLU I 517 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N MET I 519 " --> pdb=" O ASN H 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL H 38 " --> pdb=" O MET I 519 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR I 521 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 173 through 178 Processing sheet with id=AF1, first strand: chain 'H' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY H 334 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA H 319 " --> pdb=" O GLY H 334 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY H 334 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA H 319 " --> pdb=" O GLY H 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE H 218 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE H 249 " --> pdb=" O PHE H 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU H 220 " --> pdb=" O ILE H 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU H 246 " --> pdb=" O ALA H 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL H 275 " --> pdb=" O LEU H 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE H 248 " --> pdb=" O VAL H 275 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 410 through 412 Processing sheet with id=AF4, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AF5, first strand: chain 'I' and resid 47 through 49 removed outlier: 7.546A pdb=" N ASN I 36 " --> pdb=" O GLU J 517 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N MET J 519 " --> pdb=" O ASN I 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 38 " --> pdb=" O MET J 519 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N THR J 521 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 173 through 178 Processing sheet with id=AF7, first strand: chain 'I' and resid 192 through 194 removed outlier: 6.146A pdb=" N GLY I 334 " --> pdb=" O ALA I 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA I 319 " --> pdb=" O GLY I 334 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 192 through 194 removed outlier: 6.146A pdb=" N GLY I 334 " --> pdb=" O ALA I 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA I 319 " --> pdb=" O GLY I 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE I 218 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE I 249 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU I 220 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU I 246 " --> pdb=" O ALA I 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL I 275 " --> pdb=" O LEU I 246 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE I 248 " --> pdb=" O VAL I 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 410 through 412 Processing sheet with id=AG1, first strand: chain 'I' and resid 475 through 478 Processing sheet with id=AG2, first strand: chain 'J' and resid 47 through 49 removed outlier: 7.539A pdb=" N ASN J 36 " --> pdb=" O GLU K 517 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N MET K 519 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL J 38 " --> pdb=" O MET K 519 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR K 521 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 173 through 178 Processing sheet with id=AG4, first strand: chain 'J' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY J 334 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA J 319 " --> pdb=" O GLY J 334 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY J 334 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA J 319 " --> pdb=" O GLY J 334 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE J 218 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE J 249 " --> pdb=" O PHE J 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU J 220 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU J 246 " --> pdb=" O ALA J 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL J 275 " --> pdb=" O LEU J 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE J 248 " --> pdb=" O VAL J 275 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 410 through 412 Processing sheet with id=AG7, first strand: chain 'J' and resid 475 through 478 Processing sheet with id=AG8, first strand: chain 'K' and resid 47 through 49 removed outlier: 7.548A pdb=" N ASN K 36 " --> pdb=" O GLU L 517 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N MET L 519 " --> pdb=" O ASN K 36 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL K 38 " --> pdb=" O MET L 519 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR L 521 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 173 through 178 Processing sheet with id=AH1, first strand: chain 'K' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY K 334 " --> pdb=" O ALA K 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA K 319 " --> pdb=" O GLY K 334 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY K 334 " --> pdb=" O ALA K 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA K 319 " --> pdb=" O GLY K 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE K 218 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE K 249 " --> pdb=" O PHE K 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU K 220 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU K 246 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL K 275 " --> pdb=" O LEU K 246 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE K 248 " --> pdb=" O VAL K 275 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 410 through 412 Processing sheet with id=AH4, first strand: chain 'K' and resid 475 through 478 Processing sheet with id=AH5, first strand: chain 'L' and resid 47 through 49 removed outlier: 7.550A pdb=" N ASN L 36 " --> pdb=" O GLU M 517 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N MET M 519 " --> pdb=" O ASN L 36 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL L 38 " --> pdb=" O MET M 519 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR M 521 " --> pdb=" O VAL L 38 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 173 through 178 Processing sheet with id=AH7, first strand: chain 'L' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY L 334 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA L 319 " --> pdb=" O GLY L 334 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY L 334 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA L 319 " --> pdb=" O GLY L 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE L 218 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE L 249 " --> pdb=" O PHE L 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU L 220 " --> pdb=" O ILE L 249 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU L 246 " --> pdb=" O ALA L 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL L 275 " --> pdb=" O LEU L 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE L 248 " --> pdb=" O VAL L 275 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 410 through 412 Processing sheet with id=AI1, first strand: chain 'L' and resid 475 through 478 Processing sheet with id=AI2, first strand: chain 'M' and resid 47 through 49 removed outlier: 7.551A pdb=" N ASN M 36 " --> pdb=" O GLU N 517 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N MET N 519 " --> pdb=" O ASN M 36 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL M 38 " --> pdb=" O MET N 519 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR N 521 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 173 through 178 Processing sheet with id=AI4, first strand: chain 'M' and resid 192 through 194 removed outlier: 6.148A pdb=" N GLY M 334 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA M 319 " --> pdb=" O GLY M 334 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 192 through 194 removed outlier: 6.148A pdb=" N GLY M 334 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA M 319 " --> pdb=" O GLY M 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE M 218 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE M 249 " --> pdb=" O PHE M 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU M 220 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU M 246 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL M 275 " --> pdb=" O LEU M 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE M 248 " --> pdb=" O VAL M 275 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 410 through 412 Processing sheet with id=AI7, first strand: chain 'M' and resid 475 through 478 Processing sheet with id=AI8, first strand: chain 'N' and resid 173 through 178 Processing sheet with id=AI9, first strand: chain 'N' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY N 334 " --> pdb=" O ALA N 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA N 319 " --> pdb=" O GLY N 334 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 192 through 194 removed outlier: 6.147A pdb=" N GLY N 334 " --> pdb=" O ALA N 319 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA N 319 " --> pdb=" O GLY N 334 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE N 218 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE N 249 " --> pdb=" O PHE N 218 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU N 220 " --> pdb=" O ILE N 249 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU N 246 " --> pdb=" O ALA N 273 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL N 275 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE N 248 " --> pdb=" O VAL N 275 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 410 through 412 Processing sheet with id=AJ3, first strand: chain 'N' and resid 475 through 478 Processing sheet with id=AJ4, first strand: chain 'O' and resid 19 through 20 Processing sheet with id=AJ5, first strand: chain 'P' and resid 19 through 20 Processing sheet with id=AJ6, first strand: chain 'Q' and resid 19 through 20 Processing sheet with id=AJ7, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AJ8, first strand: chain 'S' and resid 19 through 20 Processing sheet with id=AJ9, first strand: chain 'T' and resid 19 through 20 Processing sheet with id=AK1, first strand: chain 'U' and resid 19 through 20 Processing sheet with id=AK2, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AK3, first strand: chain 'W' and resid 19 through 20 Processing sheet with id=AK4, first strand: chain 'X' and resid 19 through 20 Processing sheet with id=AK5, first strand: chain 'Y' and resid 19 through 20 Processing sheet with id=AK6, first strand: chain 'Z' and resid 19 through 20 Processing sheet with id=AK7, first strand: chain '1' and resid 19 through 20 Processing sheet with id=AK8, first strand: chain '2' and resid 19 through 20 3824 hydrogen bonds defined for protein. 10884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.36 Time building geometry restraints manager: 12.66 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: 19166 1.34 - 1.46: 9944 1.46 - 1.58: 26386 1.58 - 1.70: 0 1.70 - 1.82: 546 Bond restraints: 56042 Sorted by residual: bond pdb=" N MET L 388 " pdb=" CA MET L 388 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.67e+00 bond pdb=" N MET F 388 " pdb=" CA MET F 388 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.67e+00 bond pdb=" N MET D 388 " pdb=" CA MET D 388 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.65e+00 bond pdb=" N MET B 388 " pdb=" CA MET B 388 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.63e+00 bond pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.58e+00 ... (remaining 56037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 73652 1.41 - 2.83: 1437 2.83 - 4.24: 424 4.24 - 5.65: 115 5.65 - 7.07: 84 Bond angle restraints: 75712 Sorted by residual: angle pdb=" CA GLU M 396 " pdb=" CB GLU M 396 " pdb=" CG GLU M 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU F 396 " pdb=" CB GLU F 396 " pdb=" CG GLU F 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU G 396 " pdb=" CB GLU G 396 " pdb=" CG GLU G 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU B 396 " pdb=" CB GLU B 396 " pdb=" CG GLU B 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU H 396 " pdb=" CB GLU H 396 " pdb=" CG GLU H 396 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 ... (remaining 75707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 29957 16.80 - 33.60: 3149 33.60 - 50.39: 1096 50.39 - 67.19: 322 67.19 - 83.99: 126 Dihedral angle restraints: 34650 sinusoidal: 13454 harmonic: 21196 Sorted by residual: dihedral pdb=" CA ILE J 59 " pdb=" C ILE J 59 " pdb=" N GLU J 60 " pdb=" CA GLU J 60 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ILE C 59 " pdb=" C ILE C 59 " pdb=" N GLU C 60 " pdb=" CA GLU C 60 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ILE G 59 " pdb=" C ILE G 59 " pdb=" N GLU G 60 " pdb=" CA GLU G 60 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 34647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 5760 0.031 - 0.062: 2191 0.062 - 0.093: 773 0.093 - 0.125: 388 0.125 - 0.156: 30 Chirality restraints: 9142 Sorted by residual: chirality pdb=" CA MET B 388 " pdb=" N MET B 388 " pdb=" C MET B 388 " pdb=" CB MET B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA MET F 388 " pdb=" N MET F 388 " pdb=" C MET F 388 " pdb=" CB MET F 388 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA MET C 388 " pdb=" N MET C 388 " pdb=" C MET C 388 " pdb=" CB MET C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 9139 not shown) Planarity restraints: 9884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU J 256 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C GLU J 256 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU J 256 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA J 257 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 256 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C GLU I 256 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU I 256 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA I 257 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 256 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C GLU M 256 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU M 256 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA M 257 " 0.009 2.00e-02 2.50e+03 ... (remaining 9881 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 9261 2.76 - 3.30: 57192 3.30 - 3.83: 97412 3.83 - 4.37: 105873 4.37 - 4.90: 186704 Nonbonded interactions: 456442 Sorted by model distance: nonbonded pdb=" OD2 ASP C 154 " pdb=" OG1 THR C 156 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP K 154 " pdb=" OG1 THR K 156 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP B 154 " pdb=" OG1 THR B 156 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP E 154 " pdb=" OG1 THR E 156 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP D 154 " pdb=" OG1 THR D 156 " model vdw 2.225 3.040 ... (remaining 456437 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 '1' selection = chain '2' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 8.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.840 Check model and map are aligned: 0.350 Set scattering table: 0.390 Process input model: 93.070 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 56042 Z= 0.248 Angle : 0.596 7.068 75712 Z= 0.315 Chirality : 0.041 0.156 9142 Planarity : 0.003 0.023 9884 Dihedral : 16.855 83.990 21042 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.63 % Favored : 97.19 % Rotamer: Outliers : 1.61 % Allowed : 23.87 % Favored : 74.52 % 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: 1.91 (0.10), residues: 7462 helix: 2.50 (0.08), residues: 4144 sheet: 0.14 (0.18), residues: 896 loop : -0.49 (0.11), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 23 HIS 0.001 0.000 HIS 2 26 PHE 0.007 0.001 PHE B 194 TYR 0.005 0.001 TYR J 505 ARG 0.003 0.000 ARG J 321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1394 time to evaluate : 4.494 Fit side-chains REVERT: A 17 ARG cc_start: 0.7108 (ttp-110) cc_final: 0.6293 (tmt-80) REVERT: A 75 GLU cc_start: 0.7396 (tp30) cc_final: 0.6923 (tp30) REVERT: A 163 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7336 (mt-10) REVERT: A 165 MET cc_start: 0.7647 (mtm) cc_final: 0.7248 (mtt) REVERT: A 177 GLU cc_start: 0.6423 (tp30) cc_final: 0.5992 (tt0) REVERT: A 192 MET cc_start: 0.7097 (ppp) cc_final: 0.6869 (ppp) REVERT: A 224 LYS cc_start: 0.6163 (ttpp) cc_final: 0.5845 (pttp) REVERT: A 380 VAL cc_start: 0.7831 (m) cc_final: 0.7526 (m) REVERT: A 400 HIS cc_start: 0.7221 (m-70) cc_final: 0.6967 (t-90) REVERT: A 403 ARG cc_start: 0.7067 (ttm-80) cc_final: 0.6821 (ttp-170) REVERT: A 444 ARG cc_start: 0.7825 (ttp80) cc_final: 0.6812 (tpt90) REVERT: A 483 GLU cc_start: 0.7286 (pt0) cc_final: 0.7008 (mt-10) REVERT: B 17 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6302 (tmt-80) REVERT: B 75 GLU cc_start: 0.7377 (tp30) cc_final: 0.6914 (tp30) REVERT: B 163 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7410 (mt-10) REVERT: B 165 MET cc_start: 0.7655 (mtm) cc_final: 0.7216 (mtt) REVERT: B 177 GLU cc_start: 0.6447 (tp30) cc_final: 0.5948 (tt0) REVERT: B 192 MET cc_start: 0.7048 (ppp) cc_final: 0.6769 (ppp) REVERT: B 224 LYS cc_start: 0.6192 (ttpp) cc_final: 0.5876 (pttp) REVERT: B 380 VAL cc_start: 0.7796 (m) cc_final: 0.7521 (m) REVERT: B 400 HIS cc_start: 0.7253 (m-70) cc_final: 0.6997 (t-90) REVERT: B 403 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6818 (ttp-170) REVERT: B 444 ARG cc_start: 0.7856 (ttp80) cc_final: 0.6800 (tpt90) REVERT: C 17 ARG cc_start: 0.7144 (ttp-110) cc_final: 0.6351 (tmt-80) REVERT: C 75 GLU cc_start: 0.7413 (tp30) cc_final: 0.7093 (tp30) REVERT: C 163 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7407 (mt-10) REVERT: C 165 MET cc_start: 0.7669 (mtm) cc_final: 0.7163 (mtt) REVERT: C 177 GLU cc_start: 0.6477 (tp30) cc_final: 0.6060 (tt0) REVERT: C 192 MET cc_start: 0.7067 (ppp) cc_final: 0.6783 (ppp) REVERT: C 193 GLN cc_start: 0.7409 (pt0) cc_final: 0.7179 (pt0) REVERT: C 224 LYS cc_start: 0.6176 (ttpp) cc_final: 0.5916 (pttp) REVERT: C 380 VAL cc_start: 0.7861 (m) cc_final: 0.7516 (m) REVERT: C 400 HIS cc_start: 0.7214 (m-70) cc_final: 0.6964 (t-90) REVERT: C 444 ARG cc_start: 0.7828 (ttp80) cc_final: 0.6824 (tpt90) REVERT: C 494 ASP cc_start: 0.7932 (m-30) cc_final: 0.7703 (m-30) REVERT: D 17 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6279 (tmt-80) REVERT: D 75 GLU cc_start: 0.7403 (tp30) cc_final: 0.6968 (tp30) REVERT: D 163 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7401 (mt-10) REVERT: D 165 MET cc_start: 0.7643 (mtm) cc_final: 0.7257 (mtt) REVERT: D 177 GLU cc_start: 0.6432 (tp30) cc_final: 0.5999 (tt0) REVERT: D 192 MET cc_start: 0.7088 (ppp) cc_final: 0.6887 (ppp) REVERT: D 224 LYS cc_start: 0.6164 (ttpp) cc_final: 0.5809 (pttp) REVERT: D 380 VAL cc_start: 0.7847 (m) cc_final: 0.7555 (m) REVERT: D 400 HIS cc_start: 0.7308 (m-70) cc_final: 0.7024 (t-90) REVERT: D 403 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6864 (ttp-170) REVERT: D 444 ARG cc_start: 0.7819 (ttp80) cc_final: 0.6800 (tpt90) REVERT: E 17 ARG cc_start: 0.7167 (ttp-110) cc_final: 0.6356 (tmt-80) REVERT: E 75 GLU cc_start: 0.7428 (tp30) cc_final: 0.7014 (tp30) REVERT: E 165 MET cc_start: 0.7665 (mtm) cc_final: 0.7285 (mtt) REVERT: E 177 GLU cc_start: 0.6391 (tp30) cc_final: 0.5949 (tt0) REVERT: E 192 MET cc_start: 0.7044 (ppp) cc_final: 0.6819 (ppp) REVERT: E 193 GLN cc_start: 0.7349 (pt0) cc_final: 0.7143 (pt0) REVERT: E 224 LYS cc_start: 0.6099 (ttpp) cc_final: 0.5755 (pttp) REVERT: E 380 VAL cc_start: 0.7809 (m) cc_final: 0.7479 (m) REVERT: E 400 HIS cc_start: 0.7216 (m-70) cc_final: 0.6939 (t-90) REVERT: E 403 ARG cc_start: 0.7048 (ttm-80) cc_final: 0.6824 (ttp-170) REVERT: E 444 ARG cc_start: 0.7838 (ttp80) cc_final: 0.6797 (tpt90) REVERT: F 17 ARG cc_start: 0.7128 (ttp-110) cc_final: 0.6318 (tmt-80) REVERT: F 72 MET cc_start: 0.8350 (mtp) cc_final: 0.7895 (mtm) REVERT: F 75 GLU cc_start: 0.7415 (tp30) cc_final: 0.6962 (tp30) REVERT: F 163 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7431 (mt-10) REVERT: F 165 MET cc_start: 0.7760 (mtm) cc_final: 0.7211 (mtt) REVERT: F 177 GLU cc_start: 0.6436 (tp30) cc_final: 0.5896 (tt0) REVERT: F 192 MET cc_start: 0.7059 (ppp) cc_final: 0.6802 (ppp) REVERT: F 193 GLN cc_start: 0.7396 (pt0) cc_final: 0.7169 (pt0) REVERT: F 224 LYS cc_start: 0.6246 (ttpp) cc_final: 0.5973 (pttp) REVERT: F 380 VAL cc_start: 0.7841 (m) cc_final: 0.7533 (m) REVERT: F 400 HIS cc_start: 0.7274 (m-70) cc_final: 0.7051 (t-90) REVERT: F 403 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6783 (ttp-170) REVERT: F 444 ARG cc_start: 0.7789 (ttp80) cc_final: 0.6734 (tpt90) REVERT: G 17 ARG cc_start: 0.7111 (ttp-110) cc_final: 0.6274 (tmt-80) REVERT: G 75 GLU cc_start: 0.7378 (tp30) cc_final: 0.6872 (tp30) REVERT: G 163 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7335 (mt-10) REVERT: G 165 MET cc_start: 0.7685 (mtm) cc_final: 0.7161 (mtt) REVERT: G 177 GLU cc_start: 0.6490 (tp30) cc_final: 0.6004 (tt0) REVERT: G 192 MET cc_start: 0.7063 (ppp) cc_final: 0.6857 (ppp) REVERT: G 193 GLN cc_start: 0.7406 (pt0) cc_final: 0.7141 (pt0) REVERT: G 224 LYS cc_start: 0.6105 (ttpp) cc_final: 0.5795 (pttp) REVERT: G 380 VAL cc_start: 0.7893 (m) cc_final: 0.7623 (m) REVERT: G 400 HIS cc_start: 0.7276 (m-70) cc_final: 0.7027 (t-90) REVERT: G 403 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6754 (ttp-170) REVERT: G 444 ARG cc_start: 0.7843 (ttp80) cc_final: 0.6882 (tpt170) REVERT: H 17 ARG cc_start: 0.7112 (ttp-110) cc_final: 0.6311 (tmt-80) REVERT: H 75 GLU cc_start: 0.7396 (tp30) cc_final: 0.6923 (tp30) REVERT: H 163 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7336 (mt-10) REVERT: H 165 MET cc_start: 0.7649 (mtm) cc_final: 0.7248 (mtt) REVERT: H 177 GLU cc_start: 0.6420 (tp30) cc_final: 0.5986 (tt0) REVERT: H 192 MET cc_start: 0.7096 (ppp) cc_final: 0.6869 (ppp) REVERT: H 224 LYS cc_start: 0.6163 (ttpp) cc_final: 0.5846 (pttp) REVERT: H 380 VAL cc_start: 0.7840 (m) cc_final: 0.7538 (m) REVERT: H 400 HIS cc_start: 0.7227 (m-70) cc_final: 0.6971 (t-90) REVERT: H 403 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6823 (ttp-170) REVERT: H 444 ARG cc_start: 0.7824 (ttp80) cc_final: 0.6813 (tpt90) REVERT: H 483 GLU cc_start: 0.7287 (pt0) cc_final: 0.7009 (mt-10) REVERT: I 17 ARG cc_start: 0.7119 (ttp-110) cc_final: 0.6326 (tmt-80) REVERT: I 75 GLU cc_start: 0.7389 (tp30) cc_final: 0.6912 (tp30) REVERT: I 163 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7370 (mt-10) REVERT: I 165 MET cc_start: 0.7648 (mtm) cc_final: 0.7206 (mtt) REVERT: I 177 GLU cc_start: 0.6452 (tp30) cc_final: 0.5950 (tt0) REVERT: I 192 MET cc_start: 0.7049 (ppp) cc_final: 0.6768 (ppp) REVERT: I 224 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5909 (pttp) REVERT: I 380 VAL cc_start: 0.7814 (m) cc_final: 0.7546 (m) REVERT: I 400 HIS cc_start: 0.7285 (m-70) cc_final: 0.6983 (t-90) REVERT: I 403 ARG cc_start: 0.7059 (ttm-80) cc_final: 0.6797 (ttp-170) REVERT: I 444 ARG cc_start: 0.7851 (ttp80) cc_final: 0.6798 (tpt90) REVERT: J 17 ARG cc_start: 0.7139 (ttp-110) cc_final: 0.6356 (tmt-80) REVERT: J 75 GLU cc_start: 0.7414 (tp30) cc_final: 0.7095 (tp30) REVERT: J 163 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7408 (mt-10) REVERT: J 165 MET cc_start: 0.7653 (mtm) cc_final: 0.7154 (mtt) REVERT: J 177 GLU cc_start: 0.6487 (tp30) cc_final: 0.6055 (tt0) REVERT: J 192 MET cc_start: 0.7083 (ppp) cc_final: 0.6801 (ppp) REVERT: J 193 GLN cc_start: 0.7385 (pt0) cc_final: 0.7157 (pt0) REVERT: J 224 LYS cc_start: 0.6196 (ttpp) cc_final: 0.5951 (pttp) REVERT: J 380 VAL cc_start: 0.7871 (m) cc_final: 0.7527 (m) REVERT: J 400 HIS cc_start: 0.7203 (m-70) cc_final: 0.6955 (t-90) REVERT: J 444 ARG cc_start: 0.7824 (ttp80) cc_final: 0.6815 (tpt90) REVERT: J 494 ASP cc_start: 0.7954 (m-30) cc_final: 0.7748 (m-30) REVERT: K 17 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6269 (tmt-80) REVERT: K 75 GLU cc_start: 0.7390 (tp30) cc_final: 0.6961 (tp30) REVERT: K 163 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7391 (mt-10) REVERT: K 165 MET cc_start: 0.7643 (mtm) cc_final: 0.7267 (mtt) REVERT: K 177 GLU cc_start: 0.6441 (tp30) cc_final: 0.5989 (tt0) REVERT: K 192 MET cc_start: 0.7090 (ppp) cc_final: 0.6884 (ppp) REVERT: K 224 LYS cc_start: 0.6150 (ttpp) cc_final: 0.5783 (pttp) REVERT: K 380 VAL cc_start: 0.7834 (m) cc_final: 0.7540 (m) REVERT: K 400 HIS cc_start: 0.7274 (m-70) cc_final: 0.7013 (t-90) REVERT: K 403 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6866 (ttp-170) REVERT: K 444 ARG cc_start: 0.7812 (ttp80) cc_final: 0.6771 (tpt90) REVERT: L 17 ARG cc_start: 0.7158 (ttp-110) cc_final: 0.6346 (tmt-80) REVERT: L 75 GLU cc_start: 0.7415 (tp30) cc_final: 0.6982 (tp30) REVERT: L 165 MET cc_start: 0.7712 (mtm) cc_final: 0.7308 (mtt) REVERT: L 177 GLU cc_start: 0.6376 (tp30) cc_final: 0.5928 (tt0) REVERT: L 192 MET cc_start: 0.7030 (ppp) cc_final: 0.6813 (ppp) REVERT: L 224 LYS cc_start: 0.6106 (ttpp) cc_final: 0.5760 (pttp) REVERT: L 380 VAL cc_start: 0.7835 (m) cc_final: 0.7509 (m) REVERT: L 400 HIS cc_start: 0.7213 (m-70) cc_final: 0.6936 (t-90) REVERT: L 403 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6817 (ttp-170) REVERT: L 444 ARG cc_start: 0.7826 (ttp80) cc_final: 0.6783 (tpt90) REVERT: M 17 ARG cc_start: 0.7129 (ttp-110) cc_final: 0.6321 (tmt-80) REVERT: M 72 MET cc_start: 0.8348 (mtp) cc_final: 0.7904 (mtm) REVERT: M 75 GLU cc_start: 0.7408 (tp30) cc_final: 0.6948 (tp30) REVERT: M 163 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7407 (mt-10) REVERT: M 165 MET cc_start: 0.7742 (mtm) cc_final: 0.7198 (mtt) REVERT: M 177 GLU cc_start: 0.6416 (tp30) cc_final: 0.5880 (tt0) REVERT: M 192 MET cc_start: 0.7069 (ppp) cc_final: 0.6807 (ppp) REVERT: M 193 GLN cc_start: 0.7385 (pt0) cc_final: 0.7145 (pt0) REVERT: M 224 LYS cc_start: 0.6248 (ttpp) cc_final: 0.5973 (pttp) REVERT: M 380 VAL cc_start: 0.7823 (m) cc_final: 0.7516 (m) REVERT: M 400 HIS cc_start: 0.7288 (m-70) cc_final: 0.7058 (t-90) REVERT: M 403 ARG cc_start: 0.7055 (ttm-80) cc_final: 0.6793 (ttp-170) REVERT: M 444 ARG cc_start: 0.7803 (ttp80) cc_final: 0.6742 (tpt90) REVERT: M 483 GLU cc_start: 0.7211 (pt0) cc_final: 0.6994 (mt-10) REVERT: N 17 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6297 (tmt-80) REVERT: N 75 GLU cc_start: 0.7392 (tp30) cc_final: 0.6883 (tp30) REVERT: N 163 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7342 (mt-10) REVERT: N 165 MET cc_start: 0.7674 (mtm) cc_final: 0.7216 (mtt) REVERT: N 177 GLU cc_start: 0.6491 (tp30) cc_final: 0.6016 (tt0) REVERT: N 192 MET cc_start: 0.7058 (ppp) cc_final: 0.6805 (ppp) REVERT: N 193 GLN cc_start: 0.7418 (pt0) cc_final: 0.7133 (pt0) REVERT: N 224 LYS cc_start: 0.6108 (ttpp) cc_final: 0.5846 (pttp) REVERT: N 320 LYS cc_start: 0.6838 (tptt) cc_final: 0.6630 (tppt) REVERT: N 380 VAL cc_start: 0.7865 (m) cc_final: 0.7592 (m) REVERT: N 400 HIS cc_start: 0.7267 (m-70) cc_final: 0.7033 (t-90) REVERT: N 403 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6750 (ttp-170) REVERT: N 444 ARG cc_start: 0.7858 (ttp80) cc_final: 0.6883 (tpt170) REVERT: T 19 MET cc_start: 0.2668 (tpt) cc_final: 0.2439 (mmt) REVERT: Z 19 MET cc_start: 0.2738 (tpt) cc_final: 0.2526 (mmt) REVERT: 1 19 MET cc_start: 0.2680 (tpt) cc_final: 0.2437 (mmt) outliers start: 94 outliers final: 31 residues processed: 1450 average time/residue: 1.5284 time to fit residues: 2735.5499 Evaluate side-chains 948 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 917 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 324 ILE Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 232 MET Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 329 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 626 optimal weight: 2.9990 chunk 562 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 379 optimal weight: 7.9990 chunk 300 optimal weight: 5.9990 chunk 581 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 353 optimal weight: 0.8980 chunk 432 optimal weight: 6.9990 chunk 673 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN F 365 GLN G 365 GLN H 365 GLN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 56042 Z= 0.258 Angle : 0.612 7.481 75712 Z= 0.319 Chirality : 0.044 0.202 9142 Planarity : 0.004 0.030 9884 Dihedral : 4.628 46.648 7959 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.09 % Favored : 97.72 % Rotamer: Outliers : 5.25 % Allowed : 25.03 % Favored : 69.71 % 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: 1.64 (0.09), residues: 7462 helix: 2.15 (0.08), residues: 4228 sheet: -0.19 (0.15), residues: 1148 loop : -0.32 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 23 HIS 0.002 0.001 HIS L 400 PHE 0.006 0.001 PHE Z 25 TYR 0.011 0.001 TYR J 505 ARG 0.004 0.000 ARG J 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 960 time to evaluate : 4.579 Fit side-chains REVERT: A 17 ARG cc_start: 0.7232 (ttp-110) cc_final: 0.6438 (tmt-80) REVERT: A 75 GLU cc_start: 0.7399 (tp30) cc_final: 0.6912 (tp30) REVERT: A 79 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7805 (ttpt) REVERT: A 184 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6379 (m-30) REVERT: A 192 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7008 (ppp) REVERT: A 213 GLU cc_start: 0.7038 (mp0) cc_final: 0.6699 (mp0) REVERT: A 224 LYS cc_start: 0.6159 (ttpp) cc_final: 0.5874 (pttp) REVERT: A 397 ASP cc_start: 0.6815 (m-30) cc_final: 0.6537 (t0) REVERT: A 403 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6822 (ttp-170) REVERT: A 444 ARG cc_start: 0.7956 (ttp80) cc_final: 0.6843 (tpt90) REVERT: A 483 GLU cc_start: 0.7293 (pt0) cc_final: 0.7023 (mt-10) REVERT: B 17 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6436 (tmt-80) REVERT: B 75 GLU cc_start: 0.7379 (tp30) cc_final: 0.6896 (tp30) REVERT: B 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7764 (ttpt) REVERT: B 110 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.6769 (mtm) REVERT: B 184 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6413 (m-30) REVERT: B 192 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6983 (ppp) REVERT: B 213 GLU cc_start: 0.7003 (mp0) cc_final: 0.6669 (mp0) REVERT: B 224 LYS cc_start: 0.6211 (ttpp) cc_final: 0.5752 (pttp) REVERT: B 397 ASP cc_start: 0.6812 (m-30) cc_final: 0.6516 (t0) REVERT: B 403 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6771 (ttp-170) REVERT: C 17 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.6461 (tmt-80) REVERT: C 75 GLU cc_start: 0.7420 (tp30) cc_final: 0.7066 (tp30) REVERT: C 79 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7775 (ttpt) REVERT: C 165 MET cc_start: 0.7376 (mtm) cc_final: 0.7027 (mtt) REVERT: C 184 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6406 (m-30) REVERT: C 192 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6967 (ppp) REVERT: C 193 GLN cc_start: 0.7598 (pt0) cc_final: 0.7328 (pt0) REVERT: C 213 GLU cc_start: 0.7005 (mp0) cc_final: 0.6597 (mp0) REVERT: C 224 LYS cc_start: 0.6169 (ttpp) cc_final: 0.5729 (pttp) REVERT: C 397 ASP cc_start: 0.6894 (m-30) cc_final: 0.6588 (t0) REVERT: D 12 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.6320 (mtp180) REVERT: D 17 ARG cc_start: 0.7192 (ttp-110) cc_final: 0.6391 (tmt-80) REVERT: D 75 GLU cc_start: 0.7402 (tp30) cc_final: 0.6927 (tp30) REVERT: D 79 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7784 (ttpt) REVERT: D 165 MET cc_start: 0.7418 (mtm) cc_final: 0.7198 (mtt) REVERT: D 184 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6428 (m-30) REVERT: D 192 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7018 (ppp) REVERT: D 213 GLU cc_start: 0.7082 (mp0) cc_final: 0.6756 (mp0) REVERT: D 224 LYS cc_start: 0.6218 (ttpp) cc_final: 0.5741 (pttp) REVERT: D 397 ASP cc_start: 0.6840 (m-30) cc_final: 0.6567 (t0) REVERT: D 403 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6799 (ttp-170) REVERT: E 12 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6436 (mtp180) REVERT: E 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6464 (tmt-80) REVERT: E 75 GLU cc_start: 0.7478 (tp30) cc_final: 0.6945 (tp30) REVERT: E 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7773 (ttpt) REVERT: E 165 MET cc_start: 0.7504 (mtm) cc_final: 0.7303 (mtt) REVERT: E 184 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6432 (m-30) REVERT: E 190 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7232 (mm-30) REVERT: E 192 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6953 (ppp) REVERT: E 193 GLN cc_start: 0.7547 (pt0) cc_final: 0.7299 (pt0) REVERT: E 224 LYS cc_start: 0.6142 (ttpp) cc_final: 0.5775 (pttp) REVERT: E 397 ASP cc_start: 0.6833 (m-30) cc_final: 0.6532 (t0) REVERT: F 12 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6326 (mtp180) REVERT: F 17 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6407 (tmt-80) REVERT: F 75 GLU cc_start: 0.7443 (tp30) cc_final: 0.6934 (tp30) REVERT: F 79 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7784 (ttpt) REVERT: F 193 GLN cc_start: 0.7545 (pt0) cc_final: 0.7286 (pt0) REVERT: F 213 GLU cc_start: 0.7100 (mp0) cc_final: 0.6684 (mp0) REVERT: F 224 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5878 (pttp) REVERT: F 225 LYS cc_start: 0.7188 (mtmm) cc_final: 0.6560 (mtpp) REVERT: F 397 ASP cc_start: 0.6880 (m-30) cc_final: 0.6599 (t0) REVERT: F 400 HIS cc_start: 0.7321 (m-70) cc_final: 0.6988 (t-90) REVERT: F 403 ARG cc_start: 0.7083 (ttm-80) cc_final: 0.6793 (ttp-170) REVERT: F 444 ARG cc_start: 0.7896 (ttp80) cc_final: 0.6779 (tpt90) REVERT: G 12 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6618 (mtp180) REVERT: G 17 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6476 (tmt-80) REVERT: G 75 GLU cc_start: 0.7398 (tp30) cc_final: 0.6857 (tp30) REVERT: G 79 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7790 (ttpt) REVERT: G 165 MET cc_start: 0.7455 (mtm) cc_final: 0.7118 (mtt) REVERT: G 184 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: G 193 GLN cc_start: 0.7582 (pt0) cc_final: 0.7323 (pt0) REVERT: G 224 LYS cc_start: 0.6111 (ttpp) cc_final: 0.5708 (pttp) REVERT: G 264 ASN cc_start: 0.6131 (OUTLIER) cc_final: 0.5569 (t0) REVERT: G 380 VAL cc_start: 0.7913 (m) cc_final: 0.7641 (m) REVERT: G 397 ASP cc_start: 0.6818 (m-30) cc_final: 0.6510 (t0) REVERT: G 403 ARG cc_start: 0.7039 (ttm-80) cc_final: 0.6723 (ttp-170) REVERT: H 17 ARG cc_start: 0.7228 (ttp-110) cc_final: 0.6433 (tmt-80) REVERT: H 75 GLU cc_start: 0.7399 (tp30) cc_final: 0.6910 (tp30) REVERT: H 79 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7802 (ttpt) REVERT: H 184 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: H 192 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7003 (ppp) REVERT: H 213 GLU cc_start: 0.7037 (mp0) cc_final: 0.6701 (mp0) REVERT: H 224 LYS cc_start: 0.6158 (ttpp) cc_final: 0.5874 (pttp) REVERT: H 397 ASP cc_start: 0.6812 (m-30) cc_final: 0.6534 (t0) REVERT: H 403 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6820 (ttp-170) REVERT: H 444 ARG cc_start: 0.7954 (ttp80) cc_final: 0.6840 (tpt90) REVERT: H 483 GLU cc_start: 0.7295 (pt0) cc_final: 0.7025 (mt-10) REVERT: I 12 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6421 (mtp180) REVERT: I 17 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6434 (tmt-80) REVERT: I 75 GLU cc_start: 0.7381 (tp30) cc_final: 0.6892 (tp30) REVERT: I 79 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7765 (ttpt) REVERT: I 110 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.6723 (mtm) REVERT: I 184 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6411 (m-30) REVERT: I 192 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7009 (ppp) REVERT: I 213 GLU cc_start: 0.6966 (mp0) cc_final: 0.6553 (mp0) REVERT: I 224 LYS cc_start: 0.6216 (ttpp) cc_final: 0.5765 (pttp) REVERT: I 397 ASP cc_start: 0.6827 (m-30) cc_final: 0.6527 (t0) REVERT: I 403 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6776 (ttp-170) REVERT: J 17 ARG cc_start: 0.7246 (ttp-110) cc_final: 0.6444 (tmt-80) REVERT: J 75 GLU cc_start: 0.7420 (tp30) cc_final: 0.7064 (tp30) REVERT: J 79 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7784 (ttpt) REVERT: J 165 MET cc_start: 0.7368 (mtm) cc_final: 0.6978 (mtt) REVERT: J 184 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6435 (m-30) REVERT: J 192 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6965 (ppp) REVERT: J 193 GLN cc_start: 0.7592 (pt0) cc_final: 0.7320 (pt0) REVERT: J 213 GLU cc_start: 0.6969 (mp0) cc_final: 0.6521 (mp0) REVERT: J 224 LYS cc_start: 0.6203 (ttpp) cc_final: 0.5798 (pttp) REVERT: J 397 ASP cc_start: 0.6898 (m-30) cc_final: 0.6593 (t0) REVERT: K 12 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.6320 (mtp180) REVERT: K 17 ARG cc_start: 0.7193 (ttp-110) cc_final: 0.6389 (tmt-80) REVERT: K 75 GLU cc_start: 0.7404 (tp30) cc_final: 0.6928 (tp30) REVERT: K 79 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7777 (ttpt) REVERT: K 165 MET cc_start: 0.7444 (mtm) cc_final: 0.7224 (mtt) REVERT: K 184 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: K 192 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7009 (ppp) REVERT: K 224 LYS cc_start: 0.6220 (ttpp) cc_final: 0.5907 (pttp) REVERT: K 380 VAL cc_start: 0.7921 (m) cc_final: 0.7684 (m) REVERT: K 397 ASP cc_start: 0.6841 (m-30) cc_final: 0.6566 (t0) REVERT: K 403 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6780 (ttp-170) REVERT: L 12 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6434 (mtp180) REVERT: L 17 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.6467 (tmt-80) REVERT: L 75 GLU cc_start: 0.7464 (tp30) cc_final: 0.6938 (tp30) REVERT: L 79 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7776 (ttpt) REVERT: L 184 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6451 (m-30) REVERT: L 190 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7244 (mm-30) REVERT: L 192 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6965 (ppp) REVERT: L 213 GLU cc_start: 0.7102 (mp0) cc_final: 0.6756 (mp0) REVERT: L 224 LYS cc_start: 0.6153 (ttpp) cc_final: 0.5790 (pttp) REVERT: L 226 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6351 (tp) REVERT: L 397 ASP cc_start: 0.6836 (m-30) cc_final: 0.6533 (t0) REVERT: M 12 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6321 (mtp180) REVERT: M 17 ARG cc_start: 0.7215 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: M 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6930 (tp30) REVERT: M 79 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7790 (ttpt) REVERT: M 193 GLN cc_start: 0.7528 (pt0) cc_final: 0.7251 (pt0) REVERT: M 213 GLU cc_start: 0.7106 (mp0) cc_final: 0.6670 (mp0) REVERT: M 224 LYS cc_start: 0.6197 (ttpp) cc_final: 0.5864 (pttp) REVERT: M 225 LYS cc_start: 0.7160 (mtmm) cc_final: 0.6543 (mtpp) REVERT: M 397 ASP cc_start: 0.6868 (m-30) cc_final: 0.6587 (t0) REVERT: M 400 HIS cc_start: 0.7326 (m-70) cc_final: 0.6997 (t-90) REVERT: M 403 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6799 (ttp-170) REVERT: M 444 ARG cc_start: 0.7889 (ttp80) cc_final: 0.6768 (tpt90) REVERT: M 483 GLU cc_start: 0.7244 (pt0) cc_final: 0.6991 (mt-10) REVERT: N 12 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6610 (mtp180) REVERT: N 17 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6456 (tmt-80) REVERT: N 75 GLU cc_start: 0.7402 (tp30) cc_final: 0.6869 (tp30) REVERT: N 79 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7792 (ttpt) REVERT: N 165 MET cc_start: 0.7390 (mtm) cc_final: 0.6951 (mtt) REVERT: N 184 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6366 (m-30) REVERT: N 193 GLN cc_start: 0.7583 (pt0) cc_final: 0.7322 (pt0) REVERT: N 224 LYS cc_start: 0.6090 (ttpp) cc_final: 0.5703 (pttp) REVERT: N 264 ASN cc_start: 0.6135 (OUTLIER) cc_final: 0.5597 (t0) REVERT: N 320 LYS cc_start: 0.7101 (tptt) cc_final: 0.6857 (tppt) REVERT: N 380 VAL cc_start: 0.7918 (m) cc_final: 0.7648 (m) REVERT: N 397 ASP cc_start: 0.6798 (m-30) cc_final: 0.6499 (t0) REVERT: N 403 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6727 (ttp-170) outliers start: 306 outliers final: 102 residues processed: 1153 average time/residue: 1.4358 time to fit residues: 2073.8442 Evaluate side-chains 1031 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 879 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 318 GLN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 264 ASN Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 192 MET Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 232 MET Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 192 MET Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 184 ASP Chi-restraints excluded: chain L residue 192 MET Chi-restraints excluded: chain L residue 226 ILE Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 308 LEU Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 232 MET Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 299 VAL Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 232 MET Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 264 ASN Chi-restraints excluded: chain N residue 276 LYS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 374 optimal weight: 0.7980 chunk 209 optimal weight: 0.9980 chunk 560 optimal weight: 5.9990 chunk 458 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 675 optimal weight: 1.9990 chunk 729 optimal weight: 7.9990 chunk 601 optimal weight: 20.0000 chunk 669 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 541 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 365 GLN F 365 GLN G 365 GLN H 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 56042 Z= 0.181 Angle : 0.535 7.166 75712 Z= 0.280 Chirality : 0.042 0.153 9142 Planarity : 0.003 0.027 9884 Dihedral : 4.461 42.156 7946 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.35 % Favored : 97.47 % Rotamer: Outliers : 4.55 % Allowed : 24.81 % Favored : 70.64 % 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: 1.75 (0.10), residues: 7462 helix: 2.27 (0.08), residues: 4228 sheet: -0.18 (0.15), residues: 1106 loop : -0.31 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 2 23 HIS 0.002 0.001 HIS E 400 PHE 0.007 0.001 PHE Y 25 TYR 0.010 0.001 TYR C 505 ARG 0.003 0.000 ARG N 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 880 time to evaluate : 4.567 Fit side-chains REVERT: A 17 ARG cc_start: 0.7228 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: A 75 GLU cc_start: 0.7423 (tp30) cc_final: 0.6927 (tp30) REVERT: A 79 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7788 (ttpt) REVERT: A 184 ASP cc_start: 0.6787 (m-30) cc_final: 0.6443 (m-30) REVERT: A 192 MET cc_start: 0.7353 (ppp) cc_final: 0.6993 (ppp) REVERT: A 213 GLU cc_start: 0.7120 (mp0) cc_final: 0.6678 (mp0) REVERT: A 224 LYS cc_start: 0.6182 (ttpp) cc_final: 0.5815 (pttp) REVERT: A 397 ASP cc_start: 0.6838 (m-30) cc_final: 0.6577 (t0) REVERT: A 400 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: A 403 ARG cc_start: 0.7104 (ttm-80) cc_final: 0.6783 (ttp-170) REVERT: A 444 ARG cc_start: 0.7911 (ttp80) cc_final: 0.6832 (tpt90) REVERT: A 483 GLU cc_start: 0.7240 (pt0) cc_final: 0.6969 (mt-10) REVERT: B 17 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6409 (tmt-80) REVERT: B 75 GLU cc_start: 0.7402 (tp30) cc_final: 0.6908 (tp30) REVERT: B 79 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7739 (ttpt) REVERT: B 192 MET cc_start: 0.7343 (ppp) cc_final: 0.6966 (ppp) REVERT: B 213 GLU cc_start: 0.7027 (mp0) cc_final: 0.6573 (mp0) REVERT: B 224 LYS cc_start: 0.6166 (ttpp) cc_final: 0.5767 (pttp) REVERT: B 397 ASP cc_start: 0.6829 (m-30) cc_final: 0.6548 (t0) REVERT: B 403 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.6754 (ttp-170) REVERT: C 12 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6251 (mtp180) REVERT: C 17 ARG cc_start: 0.7222 (ttp-110) cc_final: 0.6412 (tmt-80) REVERT: C 75 GLU cc_start: 0.7433 (tp30) cc_final: 0.7061 (tp30) REVERT: C 79 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7794 (ttpt) REVERT: C 165 MET cc_start: 0.7290 (mtm) cc_final: 0.6995 (mtt) REVERT: C 193 GLN cc_start: 0.7570 (pt0) cc_final: 0.7353 (pt0) REVERT: C 213 GLU cc_start: 0.7056 (mp0) cc_final: 0.6755 (mp0) REVERT: C 224 LYS cc_start: 0.6188 (ttpp) cc_final: 0.5795 (pttp) REVERT: C 321 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6175 (ttt-90) REVERT: C 397 ASP cc_start: 0.6879 (m-30) cc_final: 0.6587 (t0) REVERT: C 400 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6965 (t-90) REVERT: D 12 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6306 (mtp180) REVERT: D 17 ARG cc_start: 0.7177 (ttp-110) cc_final: 0.6361 (tmt-80) REVERT: D 75 GLU cc_start: 0.7431 (tp30) cc_final: 0.6984 (tp30) REVERT: D 79 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7781 (ttpt) REVERT: D 165 MET cc_start: 0.7398 (mtm) cc_final: 0.7192 (mtt) REVERT: D 224 LYS cc_start: 0.6294 (ttpp) cc_final: 0.5790 (pttp) REVERT: D 397 ASP cc_start: 0.6856 (m-30) cc_final: 0.6549 (t0) REVERT: D 400 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.7018 (t-90) REVERT: D 403 ARG cc_start: 0.7147 (ttm-80) cc_final: 0.6788 (ttp-170) REVERT: E 12 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6368 (mtp180) REVERT: E 17 ARG cc_start: 0.7256 (ttp-110) cc_final: 0.6448 (tmt-80) REVERT: E 75 GLU cc_start: 0.7460 (tp30) cc_final: 0.6974 (tp30) REVERT: E 79 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7735 (ttpt) REVERT: E 190 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7183 (mm-30) REVERT: E 193 GLN cc_start: 0.7532 (pt0) cc_final: 0.7306 (pt0) REVERT: E 213 GLU cc_start: 0.7089 (mp0) cc_final: 0.6673 (mp0) REVERT: E 224 LYS cc_start: 0.6099 (ttpp) cc_final: 0.5762 (pttp) REVERT: E 397 ASP cc_start: 0.6786 (m-30) cc_final: 0.6512 (t0) REVERT: E 400 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6986 (t-90) REVERT: F 12 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6281 (mtp180) REVERT: F 17 ARG cc_start: 0.7197 (ttp-110) cc_final: 0.6388 (tmt-80) REVERT: F 75 GLU cc_start: 0.7460 (tp30) cc_final: 0.6940 (tp30) REVERT: F 79 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7788 (ttpt) REVERT: F 213 GLU cc_start: 0.7121 (mp0) cc_final: 0.6640 (mp0) REVERT: F 224 LYS cc_start: 0.6191 (ttpp) cc_final: 0.5880 (pttp) REVERT: F 397 ASP cc_start: 0.6825 (m-30) cc_final: 0.6561 (t0) REVERT: F 400 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.7024 (t-90) REVERT: F 403 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6738 (ttp-170) REVERT: F 444 ARG cc_start: 0.7877 (ttp80) cc_final: 0.6717 (tpt90) REVERT: G 12 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6579 (mtp180) REVERT: G 17 ARG cc_start: 0.7193 (ttp-110) cc_final: 0.6443 (tmt-80) REVERT: G 75 GLU cc_start: 0.7420 (tp30) cc_final: 0.6882 (tp30) REVERT: G 79 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7750 (ttpt) REVERT: G 165 MET cc_start: 0.7362 (mtp) cc_final: 0.7069 (mtt) REVERT: G 213 GLU cc_start: 0.7166 (mp0) cc_final: 0.6692 (mp0) REVERT: G 224 LYS cc_start: 0.6137 (ttpp) cc_final: 0.5735 (pttp) REVERT: G 264 ASN cc_start: 0.6162 (OUTLIER) cc_final: 0.5642 (t0) REVERT: G 397 ASP cc_start: 0.6788 (m-30) cc_final: 0.6497 (t0) REVERT: G 400 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.7040 (t-90) REVERT: G 403 ARG cc_start: 0.7072 (ttm-80) cc_final: 0.6740 (ttp-170) REVERT: H 17 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: H 75 GLU cc_start: 0.7410 (tp30) cc_final: 0.6912 (tp30) REVERT: H 79 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7784 (ttpt) REVERT: H 184 ASP cc_start: 0.6789 (m-30) cc_final: 0.6448 (m-30) REVERT: H 192 MET cc_start: 0.7349 (ppp) cc_final: 0.6990 (ppp) REVERT: H 213 GLU cc_start: 0.7117 (mp0) cc_final: 0.6703 (mp0) REVERT: H 224 LYS cc_start: 0.6184 (ttpp) cc_final: 0.5820 (pttp) REVERT: H 397 ASP cc_start: 0.6836 (m-30) cc_final: 0.6575 (t0) REVERT: H 400 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: H 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6781 (ttp-170) REVERT: H 444 ARG cc_start: 0.7912 (ttp80) cc_final: 0.6832 (tpt90) REVERT: H 483 GLU cc_start: 0.7243 (pt0) cc_final: 0.6972 (mt-10) REVERT: I 12 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.6371 (mtp180) REVERT: I 17 ARG cc_start: 0.7215 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: I 75 GLU cc_start: 0.7403 (tp30) cc_final: 0.6905 (tp30) REVERT: I 79 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7741 (ttpt) REVERT: I 192 MET cc_start: 0.7346 (ppp) cc_final: 0.6977 (ppp) REVERT: I 213 GLU cc_start: 0.7017 (mp0) cc_final: 0.6572 (mp0) REVERT: I 224 LYS cc_start: 0.6180 (ttpp) cc_final: 0.5784 (pttp) REVERT: I 397 ASP cc_start: 0.6834 (m-30) cc_final: 0.6561 (t0) REVERT: I 403 ARG cc_start: 0.7056 (ttm-80) cc_final: 0.6751 (ttp-170) REVERT: J 17 ARG cc_start: 0.7215 (ttp-110) cc_final: 0.6401 (tmt-80) REVERT: J 75 GLU cc_start: 0.7432 (tp30) cc_final: 0.7069 (tp30) REVERT: J 79 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7796 (ttpt) REVERT: J 165 MET cc_start: 0.7278 (mtm) cc_final: 0.7047 (mtt) REVERT: J 193 GLN cc_start: 0.7557 (pt0) cc_final: 0.7340 (pt0) REVERT: J 213 GLU cc_start: 0.7057 (mp0) cc_final: 0.6584 (mp0) REVERT: J 224 LYS cc_start: 0.6205 (ttpp) cc_final: 0.5768 (pttp) REVERT: J 397 ASP cc_start: 0.6876 (m-30) cc_final: 0.6586 (t0) REVERT: J 400 HIS cc_start: 0.7320 (OUTLIER) cc_final: 0.6958 (t-90) REVERT: K 12 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6304 (mtp180) REVERT: K 17 ARG cc_start: 0.7181 (ttp-110) cc_final: 0.6372 (tmt-80) REVERT: K 75 GLU cc_start: 0.7427 (tp30) cc_final: 0.6982 (tp30) REVERT: K 79 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7772 (ttpt) REVERT: K 213 GLU cc_start: 0.7121 (mp0) cc_final: 0.6720 (mp0) REVERT: K 224 LYS cc_start: 0.6275 (ttpp) cc_final: 0.5767 (pttp) REVERT: K 397 ASP cc_start: 0.6870 (m-30) cc_final: 0.6555 (t0) REVERT: K 400 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: K 403 ARG cc_start: 0.7143 (ttm-80) cc_final: 0.6785 (ttp-170) REVERT: L 12 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6370 (mtp180) REVERT: L 17 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: L 75 GLU cc_start: 0.7461 (tp30) cc_final: 0.6920 (tp30) REVERT: L 79 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7753 (ttpt) REVERT: L 190 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7131 (mm-30) REVERT: L 192 MET cc_start: 0.7299 (ppp) cc_final: 0.6916 (ppp) REVERT: L 224 LYS cc_start: 0.6122 (ttpp) cc_final: 0.5792 (pttp) REVERT: L 397 ASP cc_start: 0.6792 (m-30) cc_final: 0.6511 (t0) REVERT: L 400 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6969 (t-90) REVERT: M 12 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6271 (mtp180) REVERT: M 17 ARG cc_start: 0.7208 (ttp-110) cc_final: 0.6397 (tmt-80) REVERT: M 75 GLU cc_start: 0.7463 (tp30) cc_final: 0.6939 (tp30) REVERT: M 79 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7787 (ttpt) REVERT: M 224 LYS cc_start: 0.6191 (ttpp) cc_final: 0.5862 (pttp) REVERT: M 397 ASP cc_start: 0.6812 (m-30) cc_final: 0.6548 (t0) REVERT: M 400 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.7029 (t-90) REVERT: M 403 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6818 (ttp-170) REVERT: M 444 ARG cc_start: 0.7886 (ttp80) cc_final: 0.6727 (tpt90) REVERT: M 483 GLU cc_start: 0.7220 (pt0) cc_final: 0.6975 (mt-10) REVERT: N 12 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.6610 (mtp180) REVERT: N 17 ARG cc_start: 0.7192 (ttp-110) cc_final: 0.6441 (tmt-80) REVERT: N 75 GLU cc_start: 0.7417 (tp30) cc_final: 0.6877 (tp30) REVERT: N 79 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7742 (ttpt) REVERT: N 165 MET cc_start: 0.7334 (mtp) cc_final: 0.7029 (mtt) REVERT: N 224 LYS cc_start: 0.6114 (ttpp) cc_final: 0.5708 (pttp) REVERT: N 320 LYS cc_start: 0.7138 (tptt) cc_final: 0.6864 (tppt) REVERT: N 397 ASP cc_start: 0.6769 (m-30) cc_final: 0.6488 (t0) REVERT: N 400 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.7048 (t-90) REVERT: N 403 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6747 (ttp-170) outliers start: 265 outliers final: 117 residues processed: 1066 average time/residue: 1.3739 time to fit residues: 1854.9070 Evaluate side-chains 992 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 837 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 12 ARG Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 225 LYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 264 ASN Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 264 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 225 LYS Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 299 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 288 LEU Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 400 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 666 optimal weight: 0.6980 chunk 507 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 322 optimal weight: 1.9990 chunk 453 optimal weight: 9.9990 chunk 677 optimal weight: 0.6980 chunk 717 optimal weight: 0.9980 chunk 353 optimal weight: 1.9990 chunk 642 optimal weight: 0.7980 chunk 193 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN I 365 GLN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 56042 Z= 0.159 Angle : 0.516 6.974 75712 Z= 0.271 Chirality : 0.041 0.151 9142 Planarity : 0.003 0.028 9884 Dihedral : 4.417 48.359 7940 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.81 % Favored : 97.00 % Rotamer: Outliers : 4.95 % Allowed : 24.00 % Favored : 71.05 % 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: 1.81 (0.10), residues: 7462 helix: 2.33 (0.08), residues: 4228 sheet: -0.15 (0.16), residues: 1106 loop : -0.32 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 23 HIS 0.001 0.001 HIS U 26 PHE 0.009 0.001 PHE 2 25 TYR 0.010 0.001 TYR C 505 ARG 0.004 0.000 ARG F 321 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 877 time to evaluate : 4.600 Fit side-chains REVERT: A 17 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.6407 (tmt-80) REVERT: A 75 GLU cc_start: 0.7390 (tp30) cc_final: 0.6892 (tp30) REVERT: A 79 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7800 (ttpt) REVERT: A 184 ASP cc_start: 0.6786 (m-30) cc_final: 0.6477 (m-30) REVERT: A 213 GLU cc_start: 0.7198 (mp0) cc_final: 0.6764 (mp0) REVERT: A 224 LYS cc_start: 0.6222 (ttpp) cc_final: 0.5807 (pttp) REVERT: A 397 ASP cc_start: 0.6851 (m-30) cc_final: 0.6581 (t0) REVERT: A 400 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6977 (t-90) REVERT: A 403 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6748 (ttp-170) REVERT: A 444 ARG cc_start: 0.7916 (ttp80) cc_final: 0.6822 (tpt90) REVERT: A 483 GLU cc_start: 0.7230 (pt0) cc_final: 0.6991 (mt-10) REVERT: B 17 ARG cc_start: 0.7231 (ttp-110) cc_final: 0.6407 (tmt-80) REVERT: B 75 GLU cc_start: 0.7420 (tp30) cc_final: 0.6916 (tp30) REVERT: B 79 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7740 (ttpt) REVERT: B 213 GLU cc_start: 0.7069 (mp0) cc_final: 0.6661 (mp0) REVERT: B 224 LYS cc_start: 0.6149 (ttpp) cc_final: 0.5856 (pttp) REVERT: B 400 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.7006 (t-90) REVERT: B 403 ARG cc_start: 0.7097 (ttm-80) cc_final: 0.6770 (ttp-170) REVERT: C 17 ARG cc_start: 0.7223 (ttp-110) cc_final: 0.6412 (tmt-80) REVERT: C 75 GLU cc_start: 0.7416 (tp30) cc_final: 0.7071 (tp30) REVERT: C 79 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7787 (ttpt) REVERT: C 165 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.7014 (mtt) REVERT: C 213 GLU cc_start: 0.7099 (mp0) cc_final: 0.6812 (mp0) REVERT: C 224 LYS cc_start: 0.6209 (ttpp) cc_final: 0.5772 (pttp) REVERT: C 236 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5990 (mt) REVERT: C 321 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6179 (ttt-90) REVERT: C 400 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6970 (t-90) REVERT: D 12 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6362 (mtp180) REVERT: D 17 ARG cc_start: 0.7167 (ttp-110) cc_final: 0.6349 (tmt-80) REVERT: D 75 GLU cc_start: 0.7433 (tp30) cc_final: 0.6983 (tp30) REVERT: D 213 GLU cc_start: 0.7173 (mp0) cc_final: 0.6775 (mp0) REVERT: D 224 LYS cc_start: 0.6237 (ttpp) cc_final: 0.5747 (pttp) REVERT: D 397 ASP cc_start: 0.6872 (m-30) cc_final: 0.6547 (t0) REVERT: D 400 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.7022 (t-90) REVERT: D 403 ARG cc_start: 0.7110 (ttm-80) cc_final: 0.6740 (ttp-170) REVERT: E 12 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6343 (mtp180) REVERT: E 17 ARG cc_start: 0.7251 (ttp-110) cc_final: 0.6423 (tmt-80) REVERT: E 75 GLU cc_start: 0.7436 (tp30) cc_final: 0.6967 (tp30) REVERT: E 79 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7745 (ttpt) REVERT: E 213 GLU cc_start: 0.7095 (mp0) cc_final: 0.6692 (mp0) REVERT: E 224 LYS cc_start: 0.6065 (ttpp) cc_final: 0.5692 (pttp) REVERT: E 236 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5950 (mt) REVERT: E 306 MET cc_start: 0.4586 (mmp) cc_final: 0.4362 (mmp) REVERT: E 397 ASP cc_start: 0.6813 (m-30) cc_final: 0.6528 (t0) REVERT: E 400 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6981 (t-90) REVERT: F 12 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6276 (mtp180) REVERT: F 17 ARG cc_start: 0.7211 (ttp-110) cc_final: 0.6390 (tmt-80) REVERT: F 75 GLU cc_start: 0.7465 (tp30) cc_final: 0.6940 (tp30) REVERT: F 79 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7775 (ttpt) REVERT: F 190 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7317 (mm-30) REVERT: F 213 GLU cc_start: 0.7161 (mp0) cc_final: 0.6651 (mp0) REVERT: F 224 LYS cc_start: 0.6222 (ttpp) cc_final: 0.5818 (pttp) REVERT: F 397 ASP cc_start: 0.6808 (m-30) cc_final: 0.6532 (t0) REVERT: F 400 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.7023 (t-90) REVERT: F 403 ARG cc_start: 0.7054 (ttm-80) cc_final: 0.6689 (ttp-170) REVERT: F 444 ARG cc_start: 0.7904 (ttp80) cc_final: 0.6760 (tpt90) REVERT: G 12 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6556 (mtp180) REVERT: G 17 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: G 75 GLU cc_start: 0.7393 (tp30) cc_final: 0.6842 (tp30) REVERT: G 79 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7758 (ttpt) REVERT: G 165 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7081 (mtt) REVERT: G 213 GLU cc_start: 0.7157 (mp0) cc_final: 0.6695 (mp0) REVERT: G 224 LYS cc_start: 0.6197 (ttpp) cc_final: 0.5786 (pttp) REVERT: G 236 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5946 (mt) REVERT: G 397 ASP cc_start: 0.6789 (m-30) cc_final: 0.6490 (t0) REVERT: G 400 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.7042 (t-90) REVERT: G 403 ARG cc_start: 0.7086 (ttm-80) cc_final: 0.6742 (ttp-170) REVERT: H 17 ARG cc_start: 0.7231 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: H 75 GLU cc_start: 0.7393 (tp30) cc_final: 0.6894 (tp30) REVERT: H 79 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7800 (ttpt) REVERT: H 184 ASP cc_start: 0.6789 (m-30) cc_final: 0.6477 (m-30) REVERT: H 213 GLU cc_start: 0.7154 (mp0) cc_final: 0.6710 (mp0) REVERT: H 224 LYS cc_start: 0.6215 (ttpp) cc_final: 0.5802 (pttp) REVERT: H 397 ASP cc_start: 0.6849 (m-30) cc_final: 0.6581 (t0) REVERT: H 400 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6976 (t-90) REVERT: H 403 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6746 (ttp-170) REVERT: H 444 ARG cc_start: 0.7908 (ttp80) cc_final: 0.6819 (tpt90) REVERT: H 483 GLU cc_start: 0.7233 (pt0) cc_final: 0.6995 (mt-10) REVERT: I 12 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.6348 (mtp180) REVERT: I 17 ARG cc_start: 0.7227 (ttp-110) cc_final: 0.6405 (tmt-80) REVERT: I 75 GLU cc_start: 0.7424 (tp30) cc_final: 0.6916 (tp30) REVERT: I 79 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7740 (ttpt) REVERT: I 224 LYS cc_start: 0.6190 (ttpp) cc_final: 0.5801 (pttp) REVERT: I 400 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6997 (t-90) REVERT: I 403 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6762 (ttp-170) REVERT: J 17 ARG cc_start: 0.7224 (ttp-110) cc_final: 0.6410 (tmt-80) REVERT: J 75 GLU cc_start: 0.7424 (tp30) cc_final: 0.7072 (tp30) REVERT: J 79 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7790 (ttpt) REVERT: J 165 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.7019 (mtt) REVERT: J 213 GLU cc_start: 0.7091 (mp0) cc_final: 0.6658 (mp0) REVERT: J 224 LYS cc_start: 0.6191 (ttpp) cc_final: 0.5772 (pttp) REVERT: J 236 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5989 (mt) REVERT: J 400 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6968 (t-90) REVERT: K 12 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6308 (mtp180) REVERT: K 17 ARG cc_start: 0.7162 (ttp-110) cc_final: 0.6346 (tmt-80) REVERT: K 75 GLU cc_start: 0.7433 (tp30) cc_final: 0.6986 (tp30) REVERT: K 213 GLU cc_start: 0.7163 (mp0) cc_final: 0.6743 (mp0) REVERT: K 224 LYS cc_start: 0.6227 (ttpp) cc_final: 0.5737 (pttp) REVERT: K 397 ASP cc_start: 0.6847 (m-30) cc_final: 0.6530 (t0) REVERT: K 400 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.7008 (t-90) REVERT: K 403 ARG cc_start: 0.7097 (ttm-80) cc_final: 0.6739 (ttp-170) REVERT: L 12 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6343 (mtp180) REVERT: L 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: L 75 GLU cc_start: 0.7435 (tp30) cc_final: 0.6966 (tp30) REVERT: L 79 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7783 (ttpt) REVERT: L 190 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7085 (mm-30) REVERT: L 213 GLU cc_start: 0.7107 (mp0) cc_final: 0.6714 (mp0) REVERT: L 224 LYS cc_start: 0.6060 (ttpp) cc_final: 0.5736 (pttp) REVERT: L 236 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5947 (mt) REVERT: L 306 MET cc_start: 0.4581 (mmp) cc_final: 0.4362 (mmp) REVERT: L 397 ASP cc_start: 0.6827 (m-30) cc_final: 0.6530 (t0) REVERT: L 400 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6965 (t-90) REVERT: M 12 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6279 (mtp180) REVERT: M 17 ARG cc_start: 0.7205 (ttp-110) cc_final: 0.6392 (tmt-80) REVERT: M 75 GLU cc_start: 0.7464 (tp30) cc_final: 0.6937 (tp30) REVERT: M 79 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7776 (ttpt) REVERT: M 213 GLU cc_start: 0.7156 (mp0) cc_final: 0.6646 (mp0) REVERT: M 224 LYS cc_start: 0.6231 (ttpp) cc_final: 0.5820 (pttp) REVERT: M 397 ASP cc_start: 0.6808 (m-30) cc_final: 0.6526 (t0) REVERT: M 400 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.7039 (t-90) REVERT: M 403 ARG cc_start: 0.7072 (ttm-80) cc_final: 0.6689 (ttp-170) REVERT: M 444 ARG cc_start: 0.7903 (ttp80) cc_final: 0.6758 (tpt90) REVERT: M 483 GLU cc_start: 0.7209 (pt0) cc_final: 0.6960 (mt-10) REVERT: N 12 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6551 (mtp180) REVERT: N 17 ARG cc_start: 0.7208 (ttp-110) cc_final: 0.6441 (tmt-80) REVERT: N 75 GLU cc_start: 0.7401 (tp30) cc_final: 0.6855 (tp30) REVERT: N 79 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7751 (ttpt) REVERT: N 165 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.7073 (mtt) REVERT: N 213 GLU cc_start: 0.7191 (mp0) cc_final: 0.6751 (mp0) REVERT: N 224 LYS cc_start: 0.6150 (ttpp) cc_final: 0.5754 (pttp) REVERT: N 320 LYS cc_start: 0.7175 (tptt) cc_final: 0.6866 (tppt) REVERT: N 397 ASP cc_start: 0.6799 (m-30) cc_final: 0.6503 (t0) REVERT: N 400 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.7054 (t-90) REVERT: N 403 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6724 (ttp-170) outliers start: 288 outliers final: 143 residues processed: 1084 average time/residue: 1.3161 time to fit residues: 1812.2629 Evaluate side-chains 1045 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 857 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 466 ASN Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 320 LYS Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 597 optimal weight: 9.9990 chunk 407 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 534 optimal weight: 1.9990 chunk 295 optimal weight: 20.0000 chunk 612 optimal weight: 4.9990 chunk 495 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 chunk 643 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 365 GLN F 365 GLN G 318 GLN G 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 56042 Z= 0.306 Angle : 0.591 8.254 75712 Z= 0.309 Chirality : 0.044 0.153 9142 Planarity : 0.004 0.032 9884 Dihedral : 4.776 58.882 7932 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.96 % Favored : 96.85 % Rotamer: Outliers : 6.66 % Allowed : 22.66 % Favored : 70.67 % 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: 1.35 (0.09), residues: 7462 helix: 2.04 (0.08), residues: 4228 sheet: -0.58 (0.17), residues: 966 loop : -0.59 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 23 HIS 0.004 0.002 HIS K 400 PHE 0.005 0.001 PHE G 194 TYR 0.013 0.001 TYR D 505 ARG 0.004 0.000 ARG H 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 864 time to evaluate : 4.588 Fit side-chains REVERT: A 17 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6421 (tmt-80) REVERT: A 75 GLU cc_start: 0.7453 (tp30) cc_final: 0.7016 (tp30) REVERT: A 79 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7753 (ttpt) REVERT: A 213 GLU cc_start: 0.7159 (mp0) cc_final: 0.6678 (mp0) REVERT: A 224 LYS cc_start: 0.6127 (ttpp) cc_final: 0.5754 (pttp) REVERT: A 306 MET cc_start: 0.4444 (mmp) cc_final: 0.4209 (mmp) REVERT: A 400 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6891 (t-90) REVERT: A 403 ARG cc_start: 0.7060 (ttm-80) cc_final: 0.6672 (ttp-170) REVERT: A 483 GLU cc_start: 0.7251 (pt0) cc_final: 0.7006 (mt-10) REVERT: B 17 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6466 (tmt-80) REVERT: B 75 GLU cc_start: 0.7447 (tp30) cc_final: 0.6978 (tp30) REVERT: B 79 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7623 (mtmm) REVERT: B 184 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6725 (m-30) REVERT: B 224 LYS cc_start: 0.6084 (ttpp) cc_final: 0.5680 (pttp) REVERT: B 400 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.6939 (t-90) REVERT: B 403 ARG cc_start: 0.7119 (ttm-80) cc_final: 0.6698 (ttp-170) REVERT: C 17 ARG cc_start: 0.7292 (ttp-110) cc_final: 0.6483 (tmt-80) REVERT: C 75 GLU cc_start: 0.7458 (tp30) cc_final: 0.7002 (tp30) REVERT: C 79 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7705 (ttpt) REVERT: C 165 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6907 (mtt) REVERT: C 184 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6690 (m-30) REVERT: C 213 GLU cc_start: 0.7041 (mp0) cc_final: 0.6742 (mp0) REVERT: C 224 LYS cc_start: 0.6188 (ttpp) cc_final: 0.5748 (pttp) REVERT: C 236 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.6006 (mt) REVERT: C 306 MET cc_start: 0.4366 (mmp) cc_final: 0.4138 (mmp) REVERT: C 321 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6125 (ttt-90) REVERT: C 400 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6935 (t-90) REVERT: D 12 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6269 (mtp180) REVERT: D 17 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.6452 (tmt-80) REVERT: D 75 GLU cc_start: 0.7458 (tp30) cc_final: 0.7024 (tp30) REVERT: D 184 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: D 213 GLU cc_start: 0.7099 (mp0) cc_final: 0.6614 (mp0) REVERT: D 224 LYS cc_start: 0.6177 (ttpp) cc_final: 0.5706 (pttp) REVERT: D 306 MET cc_start: 0.4490 (mmp) cc_final: 0.4279 (mmp) REVERT: D 400 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.6973 (t-90) REVERT: D 403 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6681 (ttp-170) REVERT: E 12 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6397 (mtp180) REVERT: E 17 ARG cc_start: 0.7301 (ttp-110) cc_final: 0.6471 (tmt-80) REVERT: E 75 GLU cc_start: 0.7517 (tp30) cc_final: 0.7026 (tp30) REVERT: E 79 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7735 (ttpt) REVERT: E 190 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7116 (mm-30) REVERT: E 213 GLU cc_start: 0.7098 (mp0) cc_final: 0.6555 (mp0) REVERT: E 224 LYS cc_start: 0.6051 (ttpp) cc_final: 0.5680 (pttp) REVERT: E 236 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5926 (mt) REVERT: E 283 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.5735 (mpp80) REVERT: E 400 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.6953 (t-90) REVERT: F 12 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6279 (mtp180) REVERT: F 17 ARG cc_start: 0.7246 (ttp-110) cc_final: 0.6429 (tmt-80) REVERT: F 75 GLU cc_start: 0.7483 (tp30) cc_final: 0.6989 (tp30) REVERT: F 79 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7738 (ttpt) REVERT: F 184 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6632 (m-30) REVERT: F 190 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7297 (mm-30) REVERT: F 213 GLU cc_start: 0.7157 (mp0) cc_final: 0.6571 (mp0) REVERT: F 224 LYS cc_start: 0.6213 (ttpp) cc_final: 0.5876 (pttp) REVERT: F 264 ASN cc_start: 0.6012 (OUTLIER) cc_final: 0.5696 (t0) REVERT: F 306 MET cc_start: 0.4700 (mmp) cc_final: 0.4483 (mmp) REVERT: F 400 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: F 403 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6883 (mtt-85) REVERT: G 12 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.6526 (mtp180) REVERT: G 17 ARG cc_start: 0.7273 (ttp-110) cc_final: 0.6496 (tmt-80) REVERT: G 75 GLU cc_start: 0.7464 (tp30) cc_final: 0.6934 (tp30) REVERT: G 79 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7716 (ttpt) REVERT: G 184 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: G 224 LYS cc_start: 0.6127 (ttpp) cc_final: 0.5746 (pttp) REVERT: G 264 ASN cc_start: 0.6149 (OUTLIER) cc_final: 0.5893 (m-40) REVERT: G 306 MET cc_start: 0.4494 (mmp) cc_final: 0.4284 (mmp) REVERT: G 397 ASP cc_start: 0.6824 (m-30) cc_final: 0.6520 (t0) REVERT: G 400 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.7029 (t-90) REVERT: G 403 ARG cc_start: 0.7098 (ttm-80) cc_final: 0.6686 (ttp-170) REVERT: H 17 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6419 (tmt-80) REVERT: H 75 GLU cc_start: 0.7453 (tp30) cc_final: 0.7017 (tp30) REVERT: H 79 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7751 (ttpt) REVERT: H 213 GLU cc_start: 0.7146 (mp0) cc_final: 0.6653 (mp0) REVERT: H 224 LYS cc_start: 0.6123 (ttpp) cc_final: 0.5752 (pttp) REVERT: H 306 MET cc_start: 0.4449 (mmp) cc_final: 0.4213 (mmp) REVERT: H 400 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6889 (t-90) REVERT: H 403 ARG cc_start: 0.7063 (ttm-80) cc_final: 0.6673 (ttp-170) REVERT: H 483 GLU cc_start: 0.7252 (pt0) cc_final: 0.7008 (mt-10) REVERT: I 12 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.6257 (mtp180) REVERT: I 17 ARG cc_start: 0.7254 (ttp-110) cc_final: 0.6460 (tmt-80) REVERT: I 75 GLU cc_start: 0.7446 (tp30) cc_final: 0.6972 (tp30) REVERT: I 79 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7622 (mtmm) REVERT: I 184 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: I 224 LYS cc_start: 0.6112 (ttpp) cc_final: 0.5710 (pttp) REVERT: I 400 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: I 403 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6690 (ttp-170) REVERT: J 17 ARG cc_start: 0.7297 (ttp-110) cc_final: 0.6492 (tmt-80) REVERT: J 75 GLU cc_start: 0.7458 (tp30) cc_final: 0.7003 (tp30) REVERT: J 79 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7706 (ttpt) REVERT: J 165 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: J 184 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: J 213 GLU cc_start: 0.7048 (mp0) cc_final: 0.6736 (mp0) REVERT: J 224 LYS cc_start: 0.6210 (ttpp) cc_final: 0.5738 (pttp) REVERT: J 236 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5988 (mt) REVERT: J 306 MET cc_start: 0.4364 (mmp) cc_final: 0.4128 (mmp) REVERT: J 321 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6117 (ttt-90) REVERT: J 400 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6944 (t-90) REVERT: K 12 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6270 (mtp180) REVERT: K 17 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6449 (tmt-80) REVERT: K 75 GLU cc_start: 0.7452 (tp30) cc_final: 0.7018 (tp30) REVERT: K 184 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6813 (m-30) REVERT: K 213 GLU cc_start: 0.7123 (mp0) cc_final: 0.6637 (mp0) REVERT: K 224 LYS cc_start: 0.6191 (ttpp) cc_final: 0.5698 (pttp) REVERT: K 306 MET cc_start: 0.4545 (mmp) cc_final: 0.4326 (mmp) REVERT: K 400 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: K 403 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6678 (ttp-170) REVERT: L 12 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6390 (mtp180) REVERT: L 17 ARG cc_start: 0.7296 (ttp-110) cc_final: 0.6472 (tmt-80) REVERT: L 75 GLU cc_start: 0.7519 (tp30) cc_final: 0.7045 (tp30) REVERT: L 79 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7581 (mtmm) REVERT: L 184 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6766 (m-30) REVERT: L 224 LYS cc_start: 0.6016 (ttpp) cc_final: 0.5630 (pttp) REVERT: L 236 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5941 (mt) REVERT: L 283 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.5712 (mpp80) REVERT: L 400 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6957 (t-90) REVERT: M 12 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.6245 (mtp180) REVERT: M 17 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6429 (tmt-80) REVERT: M 75 GLU cc_start: 0.7475 (tp30) cc_final: 0.7030 (tp30) REVERT: M 79 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7742 (ttpt) REVERT: M 184 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6621 (m-30) REVERT: M 224 LYS cc_start: 0.6187 (ttpp) cc_final: 0.5860 (pttp) REVERT: M 264 ASN cc_start: 0.6007 (OUTLIER) cc_final: 0.5685 (t0) REVERT: M 400 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.7017 (t-90) REVERT: M 403 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6898 (mtt-85) REVERT: M 483 GLU cc_start: 0.7198 (pt0) cc_final: 0.6979 (mt-10) REVERT: N 12 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6530 (mtp180) REVERT: N 17 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6494 (tmt-80) REVERT: N 75 GLU cc_start: 0.7462 (tp30) cc_final: 0.6932 (tp30) REVERT: N 79 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7714 (ttpt) REVERT: N 184 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6721 (m-30) REVERT: N 224 LYS cc_start: 0.6126 (ttpp) cc_final: 0.5743 (pttp) REVERT: N 306 MET cc_start: 0.4496 (mmp) cc_final: 0.4282 (mmp) REVERT: N 320 LYS cc_start: 0.7182 (tptt) cc_final: 0.6873 (tppt) REVERT: N 400 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7029 (t-90) REVERT: N 403 ARG cc_start: 0.7101 (ttm-80) cc_final: 0.6698 (ttp-170) REVERT: R 26 HIS cc_start: 0.5320 (OUTLIER) cc_final: 0.5079 (t70) REVERT: S 26 HIS cc_start: 0.5387 (OUTLIER) cc_final: 0.5093 (t70) REVERT: T 26 HIS cc_start: 0.5413 (OUTLIER) cc_final: 0.5142 (t70) REVERT: Y 26 HIS cc_start: 0.5346 (OUTLIER) cc_final: 0.5080 (t70) REVERT: Z 26 HIS cc_start: 0.5416 (OUTLIER) cc_final: 0.5127 (t70) REVERT: 1 26 HIS cc_start: 0.5388 (OUTLIER) cc_final: 0.5115 (t70) outliers start: 388 outliers final: 168 residues processed: 1116 average time/residue: 1.4306 time to fit residues: 2063.1651 Evaluate side-chains 1092 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 859 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 266 MET Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 264 ASN Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 276 LYS Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 321 ARG Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 466 ASN Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 184 ASP Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 299 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 276 LYS Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain Y residue 26 HIS Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain 1 residue 26 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 241 optimal weight: 20.0000 chunk 645 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 421 optimal weight: 0.7980 chunk 177 optimal weight: 0.0020 chunk 717 optimal weight: 0.8980 chunk 595 optimal weight: 5.9990 chunk 332 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 376 optimal weight: 0.9980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 36 ASN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 36 ASN H 365 GLN J 36 ASN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 56042 Z= 0.160 Angle : 0.521 7.746 75712 Z= 0.272 Chirality : 0.041 0.154 9142 Planarity : 0.003 0.030 9884 Dihedral : 4.591 59.937 7932 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.63 % Favored : 97.19 % Rotamer: Outliers : 5.44 % Allowed : 23.78 % Favored : 70.78 % 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: 1.72 (0.10), residues: 7462 helix: 2.25 (0.08), residues: 4228 sheet: -0.10 (0.16), residues: 1106 loop : -0.40 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP U 23 HIS 0.001 0.000 HIS Q 26 PHE 0.008 0.001 PHE G 194 TYR 0.009 0.001 TYR C 505 ARG 0.004 0.000 ARG L 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 890 time to evaluate : 4.539 Fit side-chains REVERT: A 17 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6393 (tmt-80) REVERT: A 75 GLU cc_start: 0.7444 (tp30) cc_final: 0.6989 (tp30) REVERT: A 79 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7736 (ttpt) REVERT: A 193 GLN cc_start: 0.7371 (pt0) cc_final: 0.7138 (pt0) REVERT: A 213 GLU cc_start: 0.7203 (mp0) cc_final: 0.6719 (mp0) REVERT: A 224 LYS cc_start: 0.6121 (ttpp) cc_final: 0.5729 (pttp) REVERT: A 306 MET cc_start: 0.4415 (mmp) cc_final: 0.4194 (mmp) REVERT: A 400 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6901 (t-90) REVERT: A 403 ARG cc_start: 0.7083 (ttm-80) cc_final: 0.6693 (ttp-170) REVERT: A 444 ARG cc_start: 0.7989 (ttm170) cc_final: 0.6852 (tpt90) REVERT: A 483 GLU cc_start: 0.7236 (pt0) cc_final: 0.6980 (mt-10) REVERT: B 17 ARG cc_start: 0.7249 (ttp-110) cc_final: 0.6430 (tmt-80) REVERT: B 75 GLU cc_start: 0.7432 (tp30) cc_final: 0.6978 (tp30) REVERT: B 79 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7631 (ttpt) REVERT: B 165 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6765 (mtt) REVERT: B 224 LYS cc_start: 0.6101 (ttpp) cc_final: 0.5699 (pttp) REVERT: B 400 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.6970 (t-90) REVERT: B 403 ARG cc_start: 0.7119 (ttm-80) cc_final: 0.6743 (ttp-170) REVERT: C 17 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6432 (tmt-80) REVERT: C 75 GLU cc_start: 0.7462 (tp30) cc_final: 0.7121 (tp30) REVERT: C 79 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7750 (ttpt) REVERT: C 165 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6883 (mtt) REVERT: C 193 GLN cc_start: 0.7452 (pt0) cc_final: 0.7194 (pt0) REVERT: C 213 GLU cc_start: 0.7093 (mp0) cc_final: 0.6640 (mp0) REVERT: C 224 LYS cc_start: 0.6157 (ttpp) cc_final: 0.5744 (pttp) REVERT: C 236 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5920 (mt) REVERT: C 306 MET cc_start: 0.4440 (mmp) cc_final: 0.4225 (mmp) REVERT: C 400 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: D 12 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6270 (mtp180) REVERT: D 17 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6397 (tmt-80) REVERT: D 75 GLU cc_start: 0.7409 (tp30) cc_final: 0.6970 (tp30) REVERT: D 193 GLN cc_start: 0.7389 (pt0) cc_final: 0.7151 (pt0) REVERT: D 213 GLU cc_start: 0.7166 (mp0) cc_final: 0.6618 (mp0) REVERT: D 224 LYS cc_start: 0.6109 (ttpp) cc_final: 0.5667 (pttp) REVERT: D 400 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7033 (t-90) REVERT: D 403 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6730 (ttp-170) REVERT: E 12 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6360 (mtp180) REVERT: E 17 ARG cc_start: 0.7276 (ttp-110) cc_final: 0.6448 (tmt-80) REVERT: E 75 GLU cc_start: 0.7476 (tp30) cc_final: 0.7031 (tp30) REVERT: E 79 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7740 (ttpt) REVERT: E 213 GLU cc_start: 0.7154 (mp0) cc_final: 0.6630 (mp0) REVERT: E 224 LYS cc_start: 0.5950 (ttpp) cc_final: 0.5629 (pttp) REVERT: E 236 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5908 (mt) REVERT: E 283 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5787 (mpp80) REVERT: E 400 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6961 (t-90) REVERT: F 12 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6247 (mtp180) REVERT: F 17 ARG cc_start: 0.7211 (ttp-110) cc_final: 0.6392 (tmt-80) REVERT: F 75 GLU cc_start: 0.7436 (tp30) cc_final: 0.6964 (tp30) REVERT: F 79 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7720 (ttpt) REVERT: F 193 GLN cc_start: 0.7526 (pt0) cc_final: 0.7314 (pt0) REVERT: F 213 GLU cc_start: 0.7153 (mp0) cc_final: 0.6607 (mp0) REVERT: F 224 LYS cc_start: 0.6244 (ttpp) cc_final: 0.5814 (pttp) REVERT: F 264 ASN cc_start: 0.6015 (OUTLIER) cc_final: 0.5687 (t0) REVERT: F 306 MET cc_start: 0.4494 (mmp) cc_final: 0.4257 (mmp) REVERT: F 400 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: F 403 ARG cc_start: 0.7153 (ttm-80) cc_final: 0.6729 (ttp-170) REVERT: F 444 ARG cc_start: 0.7962 (ttm170) cc_final: 0.6752 (tpt90) REVERT: G 12 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6551 (mtp180) REVERT: G 17 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: G 75 GLU cc_start: 0.7466 (tp30) cc_final: 0.6919 (tp30) REVERT: G 79 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7687 (ttpt) REVERT: G 224 LYS cc_start: 0.6134 (ttpp) cc_final: 0.5696 (pttp) REVERT: G 388 MET cc_start: 0.6010 (tpt) cc_final: 0.5704 (tpp) REVERT: G 400 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.7063 (t-90) REVERT: G 403 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.6700 (ttp-170) REVERT: H 17 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6393 (tmt-80) REVERT: H 75 GLU cc_start: 0.7445 (tp30) cc_final: 0.6989 (tp30) REVERT: H 79 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7736 (ttpt) REVERT: H 193 GLN cc_start: 0.7377 (pt0) cc_final: 0.7143 (pt0) REVERT: H 213 GLU cc_start: 0.7203 (mp0) cc_final: 0.6727 (mp0) REVERT: H 224 LYS cc_start: 0.6117 (ttpp) cc_final: 0.5726 (pttp) REVERT: H 306 MET cc_start: 0.4417 (mmp) cc_final: 0.4192 (mmp) REVERT: H 400 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6900 (t-90) REVERT: H 403 ARG cc_start: 0.7082 (ttm-80) cc_final: 0.6691 (ttp-170) REVERT: H 444 ARG cc_start: 0.7991 (ttm170) cc_final: 0.6853 (tpt90) REVERT: H 483 GLU cc_start: 0.7233 (pt0) cc_final: 0.6978 (mt-10) REVERT: I 12 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6305 (mtp180) REVERT: I 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6429 (tmt-80) REVERT: I 75 GLU cc_start: 0.7429 (tp30) cc_final: 0.6973 (tp30) REVERT: I 79 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7634 (ttpt) REVERT: I 165 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6795 (mtt) REVERT: I 224 LYS cc_start: 0.6128 (ttpp) cc_final: 0.5821 (pttp) REVERT: I 400 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.6969 (t-90) REVERT: I 403 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6742 (ttp-170) REVERT: J 17 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6431 (tmt-80) REVERT: J 75 GLU cc_start: 0.7464 (tp30) cc_final: 0.7122 (tp30) REVERT: J 79 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7755 (ttpt) REVERT: J 165 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6886 (mtt) REVERT: J 193 GLN cc_start: 0.7469 (pt0) cc_final: 0.7214 (pt0) REVERT: J 213 GLU cc_start: 0.7111 (mp0) cc_final: 0.6653 (mp0) REVERT: J 224 LYS cc_start: 0.6127 (ttpp) cc_final: 0.5697 (pttp) REVERT: J 236 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5931 (mt) REVERT: J 306 MET cc_start: 0.4407 (mmp) cc_final: 0.4198 (mmp) REVERT: J 400 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6979 (t-90) REVERT: K 12 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6265 (mtp180) REVERT: K 17 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6397 (tmt-80) REVERT: K 75 GLU cc_start: 0.7403 (tp30) cc_final: 0.6967 (tp30) REVERT: K 193 GLN cc_start: 0.7403 (pt0) cc_final: 0.7151 (pt0) REVERT: K 213 GLU cc_start: 0.7168 (mp0) cc_final: 0.6619 (mp0) REVERT: K 224 LYS cc_start: 0.6109 (ttpp) cc_final: 0.5664 (pttp) REVERT: K 400 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.7035 (t-90) REVERT: K 403 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6719 (ttp-170) REVERT: L 12 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6358 (mtp180) REVERT: L 17 ARG cc_start: 0.7284 (ttp-110) cc_final: 0.6456 (tmt-80) REVERT: L 75 GLU cc_start: 0.7480 (tp30) cc_final: 0.7030 (tp30) REVERT: L 79 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7719 (ttpt) REVERT: L 193 GLN cc_start: 0.7457 (pt0) cc_final: 0.7197 (pt0) REVERT: L 213 GLU cc_start: 0.7173 (mp0) cc_final: 0.6719 (mp0) REVERT: L 224 LYS cc_start: 0.5959 (ttpp) cc_final: 0.5609 (pttp) REVERT: L 236 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5921 (mt) REVERT: L 283 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5788 (mpp80) REVERT: L 400 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.6950 (t-90) REVERT: M 12 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6257 (mtp180) REVERT: M 17 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6391 (tmt-80) REVERT: M 75 GLU cc_start: 0.7437 (tp30) cc_final: 0.6963 (tp30) REVERT: M 79 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7723 (ttpt) REVERT: M 193 GLN cc_start: 0.7524 (pt0) cc_final: 0.7322 (pt0) REVERT: M 213 GLU cc_start: 0.7183 (mp0) cc_final: 0.6600 (mp0) REVERT: M 224 LYS cc_start: 0.6211 (ttpp) cc_final: 0.5791 (pttp) REVERT: M 264 ASN cc_start: 0.6024 (OUTLIER) cc_final: 0.5691 (t0) REVERT: M 400 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: M 403 ARG cc_start: 0.7149 (ttm-80) cc_final: 0.6726 (ttp-170) REVERT: M 444 ARG cc_start: 0.7974 (ttm170) cc_final: 0.6756 (tpt90) REVERT: M 483 GLU cc_start: 0.7140 (pt0) cc_final: 0.6937 (mt-10) REVERT: N 12 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6555 (mtp180) REVERT: N 17 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6458 (tmt-80) REVERT: N 75 GLU cc_start: 0.7462 (tp30) cc_final: 0.6918 (tp30) REVERT: N 79 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7699 (ttpt) REVERT: N 224 LYS cc_start: 0.6124 (ttpp) cc_final: 0.5683 (pttp) REVERT: N 320 LYS cc_start: 0.7202 (tptt) cc_final: 0.6891 (tppt) REVERT: N 321 ARG cc_start: 0.7262 (ttm-80) cc_final: 0.7034 (ttt90) REVERT: N 400 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7062 (t-90) REVERT: N 403 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6705 (ttp-170) REVERT: O 26 HIS cc_start: 0.5284 (OUTLIER) cc_final: 0.5005 (t70) REVERT: R 26 HIS cc_start: 0.5182 (OUTLIER) cc_final: 0.4963 (t70) REVERT: S 26 HIS cc_start: 0.5341 (OUTLIER) cc_final: 0.5087 (t70) REVERT: T 26 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.5090 (t70) REVERT: V 26 HIS cc_start: 0.5289 (OUTLIER) cc_final: 0.5012 (t70) REVERT: Y 26 HIS cc_start: 0.5200 (OUTLIER) cc_final: 0.4949 (t70) REVERT: Z 19 MET cc_start: 0.3081 (mmt) cc_final: 0.2852 (tmm) REVERT: Z 26 HIS cc_start: 0.5314 (OUTLIER) cc_final: 0.5027 (t70) REVERT: 1 26 HIS cc_start: 0.5361 (OUTLIER) cc_final: 0.5109 (t70) outliers start: 317 outliers final: 154 residues processed: 1122 average time/residue: 1.2834 time to fit residues: 1841.9868 Evaluate side-chains 1084 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 875 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 419 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 264 ASN Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 419 ILE Chi-restraints excluded: chain O residue 26 HIS Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain V residue 26 HIS Chi-restraints excluded: chain W residue 26 HIS Chi-restraints excluded: chain Y residue 26 HIS Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain 1 residue 26 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 692 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 409 optimal weight: 0.9980 chunk 524 optimal weight: 0.4980 chunk 406 optimal weight: 1.9990 chunk 604 optimal weight: 6.9990 chunk 400 optimal weight: 0.9990 chunk 715 optimal weight: 6.9990 chunk 447 optimal weight: 6.9990 chunk 436 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 365 GLN D 365 GLN F 365 GLN G 36 ASN G 318 GLN G 365 GLN H 365 GLN K 365 GLN M 365 GLN N 36 ASN N 365 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56042 Z= 0.188 Angle : 0.541 8.990 75712 Z= 0.279 Chirality : 0.042 0.165 9142 Planarity : 0.003 0.030 9884 Dihedral : 4.497 54.948 7928 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.67 % Favored : 97.15 % Rotamer: Outliers : 5.15 % Allowed : 24.50 % Favored : 70.35 % 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: 1.75 (0.10), residues: 7462 helix: 2.28 (0.08), residues: 4228 sheet: -0.05 (0.16), residues: 1106 loop : -0.42 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 23 HIS 0.002 0.001 HIS L 400 PHE 0.007 0.001 PHE G 194 TYR 0.011 0.001 TYR C 505 ARG 0.005 0.000 ARG D 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 884 time to evaluate : 4.543 Fit side-chains REVERT: A 17 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6394 (tmt-80) REVERT: A 75 GLU cc_start: 0.7447 (tp30) cc_final: 0.7118 (tp30) REVERT: A 79 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7781 (ttpt) REVERT: A 193 GLN cc_start: 0.7423 (pt0) cc_final: 0.7198 (pt0) REVERT: A 213 GLU cc_start: 0.7171 (mp0) cc_final: 0.6687 (mp0) REVERT: A 224 LYS cc_start: 0.6115 (ttpp) cc_final: 0.5752 (pttp) REVERT: A 400 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6904 (t-90) REVERT: A 403 ARG cc_start: 0.7062 (ttm-80) cc_final: 0.6663 (ttp-170) REVERT: A 444 ARG cc_start: 0.7984 (ttm170) cc_final: 0.6833 (tpt90) REVERT: A 483 GLU cc_start: 0.7240 (pt0) cc_final: 0.6986 (mt-10) REVERT: B 17 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6453 (tmt-80) REVERT: B 75 GLU cc_start: 0.7428 (tp30) cc_final: 0.6966 (tp30) REVERT: B 79 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7674 (ttpt) REVERT: B 165 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6758 (mtt) REVERT: B 224 LYS cc_start: 0.6105 (ttpp) cc_final: 0.5715 (pttp) REVERT: B 400 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6986 (t-90) REVERT: B 403 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6705 (ttp-170) REVERT: C 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6458 (tmt-80) REVERT: C 75 GLU cc_start: 0.7464 (tp30) cc_final: 0.7199 (tp30) REVERT: C 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7778 (ttpt) REVERT: C 165 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6859 (mtt) REVERT: C 193 GLN cc_start: 0.7504 (pt0) cc_final: 0.7295 (pt0) REVERT: C 224 LYS cc_start: 0.6214 (ttpp) cc_final: 0.5719 (pttp) REVERT: C 236 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5962 (mt) REVERT: C 283 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5946 (mpp80) REVERT: C 306 MET cc_start: 0.4381 (mmp) cc_final: 0.4082 (mmp) REVERT: C 400 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6983 (t-90) REVERT: D 12 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6298 (mtp180) REVERT: D 17 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6412 (tmt-80) REVERT: D 75 GLU cc_start: 0.7427 (tp30) cc_final: 0.6989 (tp30) REVERT: D 193 GLN cc_start: 0.7425 (pt0) cc_final: 0.7162 (pt0) REVERT: D 213 GLU cc_start: 0.7135 (mp0) cc_final: 0.6628 (mp0) REVERT: D 224 LYS cc_start: 0.6185 (ttpp) cc_final: 0.5698 (pttp) REVERT: D 400 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7023 (t-90) REVERT: D 403 ARG cc_start: 0.7116 (ttm-80) cc_final: 0.6703 (ttp-170) REVERT: D 513 MET cc_start: 0.8450 (mtt) cc_final: 0.8193 (mtt) REVERT: E 12 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6356 (mtp180) REVERT: E 17 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: E 75 GLU cc_start: 0.7498 (tp30) cc_final: 0.7059 (tp30) REVERT: E 79 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7782 (ttpt) REVERT: E 193 GLN cc_start: 0.7514 (pt0) cc_final: 0.7262 (pt0) REVERT: E 224 LYS cc_start: 0.6049 (ttpp) cc_final: 0.5713 (pttp) REVERT: E 236 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5920 (mt) REVERT: E 283 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.5788 (mpp80) REVERT: E 306 MET cc_start: 0.4467 (mmp) cc_final: 0.4166 (mmp) REVERT: E 321 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6255 (ttt-90) REVERT: E 400 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.6950 (t-90) REVERT: F 12 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6270 (mtp180) REVERT: F 17 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6402 (tmt-80) REVERT: F 75 GLU cc_start: 0.7439 (tp30) cc_final: 0.6966 (tp30) REVERT: F 79 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7760 (ttpt) REVERT: F 224 LYS cc_start: 0.6254 (ttpp) cc_final: 0.5970 (pttp) REVERT: F 264 ASN cc_start: 0.5984 (OUTLIER) cc_final: 0.5683 (t0) REVERT: F 400 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.6981 (t-90) REVERT: F 403 ARG cc_start: 0.7089 (ttm-80) cc_final: 0.6658 (ttp-170) REVERT: F 444 ARG cc_start: 0.7980 (ttm170) cc_final: 0.6748 (tpt90) REVERT: G 12 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6548 (mtp180) REVERT: G 17 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6467 (tmt-80) REVERT: G 75 GLU cc_start: 0.7481 (tp30) cc_final: 0.6943 (tp30) REVERT: G 79 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7716 (ttpt) REVERT: G 224 LYS cc_start: 0.6176 (ttpp) cc_final: 0.5708 (pttp) REVERT: G 264 ASN cc_start: 0.6206 (OUTLIER) cc_final: 0.5945 (m-40) REVERT: G 306 MET cc_start: 0.4163 (mmp) cc_final: 0.3740 (mmp) REVERT: G 400 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.7054 (t-90) REVERT: G 403 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6696 (ttp-170) REVERT: H 17 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6393 (tmt-80) REVERT: H 75 GLU cc_start: 0.7448 (tp30) cc_final: 0.7118 (tp30) REVERT: H 79 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7780 (ttpt) REVERT: H 193 GLN cc_start: 0.7427 (pt0) cc_final: 0.7198 (pt0) REVERT: H 213 GLU cc_start: 0.7207 (mp0) cc_final: 0.6719 (mp0) REVERT: H 224 LYS cc_start: 0.6111 (ttpp) cc_final: 0.5748 (pttp) REVERT: H 400 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6902 (t-90) REVERT: H 403 ARG cc_start: 0.7063 (ttm-80) cc_final: 0.6662 (ttp-170) REVERT: H 444 ARG cc_start: 0.7991 (ttm170) cc_final: 0.6834 (tpt90) REVERT: H 483 GLU cc_start: 0.7241 (pt0) cc_final: 0.6988 (mt-10) REVERT: I 12 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6331 (mtp180) REVERT: I 17 ARG cc_start: 0.7263 (ttp-110) cc_final: 0.6451 (tmt-80) REVERT: I 75 GLU cc_start: 0.7426 (tp30) cc_final: 0.6962 (tp30) REVERT: I 79 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7677 (ttpt) REVERT: I 165 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6747 (mtt) REVERT: I 224 LYS cc_start: 0.6103 (ttpp) cc_final: 0.5807 (pttp) REVERT: I 400 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.6964 (t-90) REVERT: I 403 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6706 (ttp-170) REVERT: J 17 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6456 (tmt-80) REVERT: J 75 GLU cc_start: 0.7451 (tp30) cc_final: 0.7180 (tp30) REVERT: J 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7779 (ttpt) REVERT: J 165 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6862 (mtt) REVERT: J 193 GLN cc_start: 0.7498 (pt0) cc_final: 0.7288 (pt0) REVERT: J 224 LYS cc_start: 0.6213 (ttpp) cc_final: 0.5730 (pttp) REVERT: J 236 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5944 (mt) REVERT: J 306 MET cc_start: 0.4412 (mmp) cc_final: 0.4113 (mmp) REVERT: J 400 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.6978 (t-90) REVERT: K 12 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6298 (mtp180) REVERT: K 17 ARG cc_start: 0.7250 (ttp-110) cc_final: 0.6411 (tmt-80) REVERT: K 75 GLU cc_start: 0.7431 (tp30) cc_final: 0.6992 (tp30) REVERT: K 193 GLN cc_start: 0.7422 (pt0) cc_final: 0.7147 (pt0) REVERT: K 213 GLU cc_start: 0.7117 (mp0) cc_final: 0.6618 (mp0) REVERT: K 224 LYS cc_start: 0.6160 (ttpp) cc_final: 0.5671 (pttp) REVERT: K 400 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.7027 (t-90) REVERT: K 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6648 (ttp-110) REVERT: K 513 MET cc_start: 0.8446 (mtt) cc_final: 0.8192 (mtt) REVERT: L 12 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6323 (mtp180) REVERT: L 17 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: L 75 GLU cc_start: 0.7501 (tp30) cc_final: 0.7058 (tp30) REVERT: L 79 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7825 (ttpt) REVERT: L 193 GLN cc_start: 0.7484 (pt0) cc_final: 0.7224 (pt0) REVERT: L 224 LYS cc_start: 0.5994 (ttpp) cc_final: 0.5660 (pttp) REVERT: L 236 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5890 (mt) REVERT: L 283 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.5799 (mpp80) REVERT: L 306 MET cc_start: 0.4407 (mmp) cc_final: 0.4104 (mmp) REVERT: L 400 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6958 (t-90) REVERT: M 12 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6270 (mtp180) REVERT: M 17 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6400 (tmt-80) REVERT: M 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6966 (tp30) REVERT: M 79 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7763 (ttpt) REVERT: M 193 GLN cc_start: 0.7526 (pt0) cc_final: 0.7318 (pt0) REVERT: M 224 LYS cc_start: 0.6239 (ttpp) cc_final: 0.5956 (pttp) REVERT: M 264 ASN cc_start: 0.5980 (OUTLIER) cc_final: 0.5680 (t0) REVERT: M 400 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6938 (t-90) REVERT: M 403 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6657 (ttp-170) REVERT: M 444 ARG cc_start: 0.7977 (ttm170) cc_final: 0.6743 (tpt90) REVERT: M 483 GLU cc_start: 0.7153 (pt0) cc_final: 0.6953 (mt-10) REVERT: N 12 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6551 (mtp180) REVERT: N 17 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6466 (tmt-80) REVERT: N 75 GLU cc_start: 0.7479 (tp30) cc_final: 0.6942 (tp30) REVERT: N 79 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7712 (ttpt) REVERT: N 224 LYS cc_start: 0.6165 (ttpp) cc_final: 0.5701 (pttp) REVERT: N 306 MET cc_start: 0.4182 (mmp) cc_final: 0.3766 (mmp) REVERT: N 320 LYS cc_start: 0.7207 (tptt) cc_final: 0.6890 (tppt) REVERT: N 321 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.6912 (ttt-90) REVERT: N 400 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.7055 (t-90) REVERT: N 403 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6697 (ttp-170) REVERT: R 26 HIS cc_start: 0.5198 (OUTLIER) cc_final: 0.4986 (t70) REVERT: S 26 HIS cc_start: 0.5392 (OUTLIER) cc_final: 0.5128 (t70) REVERT: T 19 MET cc_start: 0.4148 (tmm) cc_final: 0.3806 (mmt) REVERT: T 26 HIS cc_start: 0.5367 (OUTLIER) cc_final: 0.5117 (t70) REVERT: Y 26 HIS cc_start: 0.5201 (OUTLIER) cc_final: 0.4965 (t70) REVERT: Z 26 HIS cc_start: 0.5408 (OUTLIER) cc_final: 0.5144 (t70) REVERT: 1 19 MET cc_start: 0.4102 (tmm) cc_final: 0.3777 (mmt) REVERT: 1 26 HIS cc_start: 0.5371 (OUTLIER) cc_final: 0.5121 (t70) outliers start: 300 outliers final: 172 residues processed: 1092 average time/residue: 1.3251 time to fit residues: 1854.5622 Evaluate side-chains 1106 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 878 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 264 ASN Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 419 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 264 ASN Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 368 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain W residue 26 HIS Chi-restraints excluded: chain Y residue 26 HIS Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain 1 residue 26 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 442 optimal weight: 6.9990 chunk 285 optimal weight: 30.0000 chunk 427 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 454 optimal weight: 0.8980 chunk 487 optimal weight: 9.9990 chunk 353 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 562 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN I 36 ASN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 56042 Z= 0.143 Angle : 0.521 8.820 75712 Z= 0.269 Chirality : 0.041 0.157 9142 Planarity : 0.003 0.031 9884 Dihedral : 4.341 50.287 7928 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Rotamer: Outliers : 5.00 % Allowed : 24.93 % Favored : 70.07 % 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: 1.92 (0.10), residues: 7462 helix: 2.41 (0.08), residues: 4228 sheet: 0.07 (0.17), residues: 1106 loop : -0.37 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 23 HIS 0.001 0.000 HIS Q 26 PHE 0.008 0.001 PHE G 194 TYR 0.008 0.001 TYR C 505 ARG 0.005 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 900 time to evaluate : 5.117 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6408 (tmt-80) REVERT: A 75 GLU cc_start: 0.7417 (tp30) cc_final: 0.7152 (tp30) REVERT: A 79 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7821 (ttpt) REVERT: A 193 GLN cc_start: 0.7408 (pt0) cc_final: 0.7196 (pt0) REVERT: A 213 GLU cc_start: 0.7236 (mp0) cc_final: 0.6765 (mp0) REVERT: A 224 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5760 (pttp) REVERT: A 400 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: A 403 ARG cc_start: 0.7051 (ttm-80) cc_final: 0.6656 (ttp-170) REVERT: A 444 ARG cc_start: 0.8024 (ttm170) cc_final: 0.6842 (tpt90) REVERT: A 483 GLU cc_start: 0.7200 (pt0) cc_final: 0.6985 (mt-10) REVERT: B 17 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6417 (tmt-80) REVERT: B 75 GLU cc_start: 0.7408 (tp30) cc_final: 0.6938 (tp30) REVERT: B 79 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7667 (ttpt) REVERT: B 224 LYS cc_start: 0.6219 (ttpp) cc_final: 0.5788 (pttp) REVERT: B 400 HIS cc_start: 0.7404 (OUTLIER) cc_final: 0.7000 (t-90) REVERT: B 403 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6706 (ttp-170) REVERT: B 444 ARG cc_start: 0.8074 (ttm170) cc_final: 0.6830 (tpt90) REVERT: C 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6437 (tmt-80) REVERT: C 75 GLU cc_start: 0.7415 (tp30) cc_final: 0.7143 (tp30) REVERT: C 165 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6801 (mtt) REVERT: C 193 GLN cc_start: 0.7595 (pt0) cc_final: 0.7302 (pt0) REVERT: C 224 LYS cc_start: 0.6188 (ttpp) cc_final: 0.5755 (pttp) REVERT: C 236 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5941 (mt) REVERT: C 306 MET cc_start: 0.4398 (mmp) cc_final: 0.4131 (mmp) REVERT: C 400 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6987 (t-90) REVERT: D 12 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6314 (mtp180) REVERT: D 17 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6412 (tmt-80) REVERT: D 75 GLU cc_start: 0.7417 (tp30) cc_final: 0.6981 (tp30) REVERT: D 193 GLN cc_start: 0.7393 (pt0) cc_final: 0.7145 (pt0) REVERT: D 213 GLU cc_start: 0.7238 (mp0) cc_final: 0.6687 (mp0) REVERT: D 224 LYS cc_start: 0.6177 (ttpp) cc_final: 0.5733 (pttp) REVERT: D 400 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7037 (t-90) REVERT: D 403 ARG cc_start: 0.7098 (ttm-80) cc_final: 0.6681 (ttp-170) REVERT: D 444 ARG cc_start: 0.8009 (ttm170) cc_final: 0.6753 (tpt90) REVERT: D 513 MET cc_start: 0.8442 (mtt) cc_final: 0.8170 (mtt) REVERT: E 12 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6330 (mtp180) REVERT: E 17 ARG cc_start: 0.7263 (ttp-110) cc_final: 0.6434 (tmt-80) REVERT: E 75 GLU cc_start: 0.7440 (tp30) cc_final: 0.6992 (tp30) REVERT: E 193 GLN cc_start: 0.7441 (pt0) cc_final: 0.7202 (pt0) REVERT: E 224 LYS cc_start: 0.6016 (ttpp) cc_final: 0.5702 (pttp) REVERT: E 236 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5899 (mt) REVERT: E 283 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5833 (mpp80) REVERT: E 400 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6993 (t-90) REVERT: F 12 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6258 (mtp180) REVERT: F 17 ARG cc_start: 0.7210 (ttp-110) cc_final: 0.6387 (tmt-80) REVERT: F 75 GLU cc_start: 0.7425 (tp30) cc_final: 0.6902 (tp30) REVERT: F 79 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7796 (ttpt) REVERT: F 224 LYS cc_start: 0.6292 (ttpp) cc_final: 0.5981 (pttp) REVERT: F 264 ASN cc_start: 0.5946 (OUTLIER) cc_final: 0.5714 (m-40) REVERT: F 400 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.7003 (t-90) REVERT: F 403 ARG cc_start: 0.7086 (ttm-80) cc_final: 0.6708 (ttp-170) REVERT: F 444 ARG cc_start: 0.7970 (ttm170) cc_final: 0.6753 (tpt90) REVERT: G 12 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6537 (mtp180) REVERT: G 17 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6446 (tmt-80) REVERT: G 75 GLU cc_start: 0.7435 (tp30) cc_final: 0.6894 (tp30) REVERT: G 79 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7727 (ttpt) REVERT: G 224 LYS cc_start: 0.6149 (ttpp) cc_final: 0.5730 (pttp) REVERT: G 306 MET cc_start: 0.4143 (mmp) cc_final: 0.3893 (mmp) REVERT: G 321 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.6973 (ttt90) REVERT: G 388 MET cc_start: 0.5938 (tpt) cc_final: 0.5734 (tpp) REVERT: G 400 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.7082 (t-90) REVERT: G 403 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6726 (ttp-170) REVERT: G 444 ARG cc_start: 0.8032 (ttm170) cc_final: 0.6775 (tpt90) REVERT: H 17 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6410 (tmt-80) REVERT: H 75 GLU cc_start: 0.7417 (tp30) cc_final: 0.7152 (tp30) REVERT: H 79 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7821 (ttpt) REVERT: H 193 GLN cc_start: 0.7412 (pt0) cc_final: 0.7198 (pt0) REVERT: H 224 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5760 (pttp) REVERT: H 400 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6927 (t-90) REVERT: H 403 ARG cc_start: 0.7050 (ttm-80) cc_final: 0.6654 (ttp-170) REVERT: H 444 ARG cc_start: 0.8019 (ttm170) cc_final: 0.6832 (tpt90) REVERT: H 483 GLU cc_start: 0.7200 (pt0) cc_final: 0.6986 (mt-10) REVERT: I 12 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6316 (mtp180) REVERT: I 17 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6419 (tmt-80) REVERT: I 75 GLU cc_start: 0.7396 (tp30) cc_final: 0.6922 (tp30) REVERT: I 79 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7668 (ttpt) REVERT: I 224 LYS cc_start: 0.6214 (ttpp) cc_final: 0.5788 (pttp) REVERT: I 400 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.6988 (t-90) REVERT: I 403 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6736 (ttp-170) REVERT: I 444 ARG cc_start: 0.8069 (ttm170) cc_final: 0.6827 (tpt90) REVERT: J 17 ARG cc_start: 0.7250 (ttp-110) cc_final: 0.6437 (tmt-80) REVERT: J 75 GLU cc_start: 0.7416 (tp30) cc_final: 0.7143 (tp30) REVERT: J 165 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6798 (mtt) REVERT: J 193 GLN cc_start: 0.7600 (pt0) cc_final: 0.7306 (pt0) REVERT: J 224 LYS cc_start: 0.6192 (ttpp) cc_final: 0.5763 (pttp) REVERT: J 236 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5921 (mt) REVERT: J 283 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.5965 (mpp80) REVERT: J 306 MET cc_start: 0.4428 (mmp) cc_final: 0.4161 (mmp) REVERT: J 400 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6994 (t-90) REVERT: K 12 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6314 (mtp180) REVERT: K 17 ARG cc_start: 0.7254 (ttp-110) cc_final: 0.6409 (tmt-80) REVERT: K 75 GLU cc_start: 0.7419 (tp30) cc_final: 0.6984 (tp30) REVERT: K 193 GLN cc_start: 0.7399 (pt0) cc_final: 0.7130 (pt0) REVERT: K 213 GLU cc_start: 0.7212 (mp0) cc_final: 0.6728 (mp0) REVERT: K 224 LYS cc_start: 0.6152 (ttpp) cc_final: 0.5721 (pttp) REVERT: K 400 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.7028 (t-90) REVERT: K 403 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6680 (ttp-170) REVERT: K 444 ARG cc_start: 0.8009 (ttm170) cc_final: 0.6752 (tpt90) REVERT: K 513 MET cc_start: 0.8441 (mtt) cc_final: 0.8168 (mtt) REVERT: L 12 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6338 (mtp180) REVERT: L 17 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6428 (tmt-80) REVERT: L 75 GLU cc_start: 0.7440 (tp30) cc_final: 0.6990 (tp30) REVERT: L 79 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7823 (ttpt) REVERT: L 193 GLN cc_start: 0.7453 (pt0) cc_final: 0.7219 (pt0) REVERT: L 224 LYS cc_start: 0.6072 (ttpp) cc_final: 0.5658 (pttp) REVERT: L 236 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5971 (mt) REVERT: L 283 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5772 (mpp80) REVERT: L 400 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6981 (t-90) REVERT: M 12 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.6242 (mtp180) REVERT: M 17 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6382 (tmt-80) REVERT: M 75 GLU cc_start: 0.7424 (tp30) cc_final: 0.6902 (tp30) REVERT: M 79 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7798 (ttpt) REVERT: M 193 GLN cc_start: 0.7502 (pt0) cc_final: 0.7279 (pt0) REVERT: M 213 GLU cc_start: 0.7204 (mp0) cc_final: 0.6659 (mp0) REVERT: M 224 LYS cc_start: 0.6297 (ttpp) cc_final: 0.5981 (pttp) REVERT: M 264 ASN cc_start: 0.5947 (OUTLIER) cc_final: 0.5716 (m-40) REVERT: M 400 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.6994 (t-90) REVERT: M 403 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6708 (ttp-170) REVERT: M 444 ARG cc_start: 0.7985 (ttm170) cc_final: 0.6766 (tpt90) REVERT: N 12 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6517 (mtp180) REVERT: N 17 ARG cc_start: 0.7231 (ttp-110) cc_final: 0.6442 (tmt-80) REVERT: N 75 GLU cc_start: 0.7429 (tp30) cc_final: 0.6891 (tp30) REVERT: N 79 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7728 (ttpt) REVERT: N 224 LYS cc_start: 0.6157 (ttpp) cc_final: 0.5748 (pttp) REVERT: N 306 MET cc_start: 0.4234 (mmp) cc_final: 0.3967 (mmp) REVERT: N 320 LYS cc_start: 0.7191 (tptt) cc_final: 0.6876 (tppt) REVERT: N 321 ARG cc_start: 0.7235 (ttm-80) cc_final: 0.6954 (ttt-90) REVERT: N 400 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.7061 (t-90) REVERT: N 403 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6721 (ttp-170) REVERT: N 444 ARG cc_start: 0.8032 (ttm170) cc_final: 0.6781 (tpt90) REVERT: R 26 HIS cc_start: 0.5173 (OUTLIER) cc_final: 0.4956 (t70) REVERT: S 26 HIS cc_start: 0.5291 (OUTLIER) cc_final: 0.5040 (t70) REVERT: T 19 MET cc_start: 0.4255 (tmm) cc_final: 0.3932 (mmt) REVERT: T 26 HIS cc_start: 0.5246 (OUTLIER) cc_final: 0.4971 (t70) REVERT: Y 26 HIS cc_start: 0.5165 (OUTLIER) cc_final: 0.4955 (t70) REVERT: Z 26 HIS cc_start: 0.5336 (OUTLIER) cc_final: 0.5087 (t70) REVERT: 1 19 MET cc_start: 0.4243 (tmm) cc_final: 0.3927 (mmt) REVERT: 1 26 HIS cc_start: 0.5252 (OUTLIER) cc_final: 0.4978 (t70) outliers start: 291 outliers final: 142 residues processed: 1113 average time/residue: 1.2505 time to fit residues: 1789.5021 Evaluate side-chains 1077 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 886 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain Y residue 26 HIS Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain 1 residue 26 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 650 optimal weight: 7.9990 chunk 685 optimal weight: 2.9990 chunk 625 optimal weight: 0.7980 chunk 666 optimal weight: 0.5980 chunk 684 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 523 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 602 optimal weight: 9.9990 chunk 630 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 318 GLN H 365 GLN J 365 GLN K 365 GLN L 365 GLN M 365 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 56042 Z= 0.255 Angle : 0.592 11.983 75712 Z= 0.304 Chirality : 0.043 0.178 9142 Planarity : 0.004 0.032 9884 Dihedral : 4.412 53.414 7924 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.59 % Favored : 97.23 % Rotamer: Outliers : 4.43 % Allowed : 25.77 % Favored : 69.80 % 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: 1.64 (0.10), residues: 7462 helix: 2.24 (0.08), residues: 4228 sheet: -0.13 (0.16), residues: 1106 loop : -0.56 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 23 HIS 0.003 0.002 HIS C 400 PHE 0.006 0.001 PHE G 194 TYR 0.012 0.001 TYR K 505 ARG 0.006 0.000 ARG I 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 901 time to evaluate : 4.636 Fit side-chains REVERT: A 17 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6407 (tmt-80) REVERT: A 75 GLU cc_start: 0.7457 (tp30) cc_final: 0.7009 (tp30) REVERT: A 79 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7805 (ttpt) REVERT: A 213 GLU cc_start: 0.7190 (mp0) cc_final: 0.6687 (mp0) REVERT: A 224 LYS cc_start: 0.6196 (ttpp) cc_final: 0.5716 (pttp) REVERT: A 288 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6608 (mp) REVERT: A 400 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: A 403 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6610 (ttp-110) REVERT: A 483 GLU cc_start: 0.7244 (pt0) cc_final: 0.7028 (mt-10) REVERT: B 17 ARG cc_start: 0.7272 (ttp-110) cc_final: 0.6452 (tmt-80) REVERT: B 75 GLU cc_start: 0.7439 (tp30) cc_final: 0.6992 (tp30) REVERT: B 79 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7605 (mtmm) REVERT: B 224 LYS cc_start: 0.6238 (ttpp) cc_final: 0.5939 (pttp) REVERT: B 400 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6967 (t-90) REVERT: B 403 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6660 (ttp-170) REVERT: C 17 ARG cc_start: 0.7286 (ttp-110) cc_final: 0.6466 (tmt-80) REVERT: C 75 GLU cc_start: 0.7458 (tp30) cc_final: 0.7142 (tp30) REVERT: C 165 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6855 (mtt) REVERT: C 193 GLN cc_start: 0.7559 (pt0) cc_final: 0.7248 (pt0) REVERT: C 224 LYS cc_start: 0.6190 (ttpp) cc_final: 0.5712 (pttp) REVERT: C 236 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5997 (mt) REVERT: C 283 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.5912 (mpp80) REVERT: C 400 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6951 (t-90) REVERT: D 12 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6308 (mtp180) REVERT: D 17 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.6460 (tmt-80) REVERT: D 75 GLU cc_start: 0.7454 (tp30) cc_final: 0.7014 (tp30) REVERT: D 193 GLN cc_start: 0.7446 (pt0) cc_final: 0.7147 (pt0) REVERT: D 224 LYS cc_start: 0.6168 (ttpp) cc_final: 0.5736 (pttp) REVERT: D 400 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6987 (t-90) REVERT: D 403 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6629 (ttp-110) REVERT: E 12 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6352 (mtp180) REVERT: E 17 ARG cc_start: 0.7297 (ttp-110) cc_final: 0.6477 (tmt-80) REVERT: E 75 GLU cc_start: 0.7492 (tp30) cc_final: 0.7069 (tp30) REVERT: E 224 LYS cc_start: 0.6118 (ttpp) cc_final: 0.5723 (pttp) REVERT: E 236 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5888 (mt) REVERT: E 283 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.5748 (mpp80) REVERT: E 306 MET cc_start: 0.4402 (mmp) cc_final: 0.4174 (mmp) REVERT: E 400 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.6917 (t-90) REVERT: F 12 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6270 (mtp180) REVERT: F 17 ARG cc_start: 0.7227 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: F 75 GLU cc_start: 0.7447 (tp30) cc_final: 0.6932 (tp30) REVERT: F 79 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7780 (ttpt) REVERT: F 193 GLN cc_start: 0.7490 (pt0) cc_final: 0.7209 (pt0) REVERT: F 224 LYS cc_start: 0.6259 (ttpp) cc_final: 0.5981 (pttp) REVERT: F 264 ASN cc_start: 0.5915 (OUTLIER) cc_final: 0.5607 (t0) REVERT: F 400 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6976 (t-90) REVERT: F 403 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.6653 (ttp-170) REVERT: G 12 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6569 (mtp180) REVERT: G 17 ARG cc_start: 0.7279 (ttp-110) cc_final: 0.6480 (tmt-80) REVERT: G 75 GLU cc_start: 0.7489 (tp30) cc_final: 0.6953 (tp30) REVERT: G 79 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7723 (ttpt) REVERT: G 224 LYS cc_start: 0.6192 (ttpp) cc_final: 0.5735 (pttp) REVERT: G 321 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.7036 (ttt-90) REVERT: G 400 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.7062 (t-90) REVERT: G 403 ARG cc_start: 0.7119 (ttm-80) cc_final: 0.6698 (ttp-170) REVERT: H 17 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: H 75 GLU cc_start: 0.7459 (tp30) cc_final: 0.7010 (tp30) REVERT: H 79 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7805 (ttpt) REVERT: H 224 LYS cc_start: 0.6194 (ttpp) cc_final: 0.5713 (pttp) REVERT: H 288 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6607 (mp) REVERT: H 400 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: H 403 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6609 (ttp-110) REVERT: H 483 GLU cc_start: 0.7253 (pt0) cc_final: 0.7040 (mt-10) REVERT: I 12 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6266 (mtp180) REVERT: I 17 ARG cc_start: 0.7272 (ttp-110) cc_final: 0.6454 (tmt-80) REVERT: I 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6988 (tp30) REVERT: I 79 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7607 (mtmm) REVERT: I 224 LYS cc_start: 0.6221 (ttpp) cc_final: 0.5934 (pttp) REVERT: I 403 ARG cc_start: 0.7100 (ttm-80) cc_final: 0.6683 (ttp-170) REVERT: J 17 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.6463 (tmt-80) REVERT: J 75 GLU cc_start: 0.7463 (tp30) cc_final: 0.7144 (tp30) REVERT: J 165 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6852 (mtt) REVERT: J 193 GLN cc_start: 0.7558 (pt0) cc_final: 0.7238 (pt0) REVERT: J 224 LYS cc_start: 0.6173 (ttpp) cc_final: 0.5707 (pttp) REVERT: J 236 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5973 (mt) REVERT: J 283 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.5936 (mpp80) REVERT: J 400 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.6948 (t-90) REVERT: K 12 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6308 (mtp180) REVERT: K 17 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6461 (tmt-80) REVERT: K 75 GLU cc_start: 0.7447 (tp30) cc_final: 0.7011 (tp30) REVERT: K 193 GLN cc_start: 0.7450 (pt0) cc_final: 0.7136 (pt0) REVERT: K 224 LYS cc_start: 0.6182 (ttpp) cc_final: 0.5739 (pttp) REVERT: K 400 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6998 (t-90) REVERT: K 403 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.6629 (ttp-110) REVERT: L 12 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6344 (mtp180) REVERT: L 17 ARG cc_start: 0.7303 (ttp-110) cc_final: 0.6477 (tmt-80) REVERT: L 75 GLU cc_start: 0.7506 (tp30) cc_final: 0.7064 (tp30) REVERT: L 79 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7792 (ttpt) REVERT: L 193 GLN cc_start: 0.7432 (pt0) cc_final: 0.7163 (pt0) REVERT: L 224 LYS cc_start: 0.6135 (ttpp) cc_final: 0.5671 (pttp) REVERT: L 236 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5971 (mt) REVERT: L 283 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5743 (mpp80) REVERT: L 400 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6918 (t-90) REVERT: M 12 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.6266 (mtp180) REVERT: M 17 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6399 (tmt-80) REVERT: M 75 GLU cc_start: 0.7437 (tp30) cc_final: 0.6924 (tp30) REVERT: M 79 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7784 (ttpt) REVERT: M 224 LYS cc_start: 0.6251 (ttpp) cc_final: 0.5970 (pttp) REVERT: M 264 ASN cc_start: 0.5941 (OUTLIER) cc_final: 0.5636 (t0) REVERT: M 400 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: M 403 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6687 (ttp-170) REVERT: N 12 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6572 (mtp180) REVERT: N 17 ARG cc_start: 0.7276 (ttp-110) cc_final: 0.6476 (tmt-80) REVERT: N 75 GLU cc_start: 0.7486 (tp30) cc_final: 0.6951 (tp30) REVERT: N 79 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7724 (ttpt) REVERT: N 224 LYS cc_start: 0.6231 (ttpp) cc_final: 0.5748 (pttp) REVERT: N 320 LYS cc_start: 0.7205 (tptt) cc_final: 0.6873 (tppt) REVERT: N 321 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6986 (ttt-90) REVERT: N 400 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.7040 (t-90) REVERT: N 403 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6701 (ttp-170) REVERT: R 26 HIS cc_start: 0.5194 (OUTLIER) cc_final: 0.4970 (t70) REVERT: S 19 MET cc_start: 0.4202 (tmm) cc_final: 0.3762 (mmt) REVERT: S 26 HIS cc_start: 0.5456 (OUTLIER) cc_final: 0.5171 (t70) REVERT: T 19 MET cc_start: 0.4296 (tmm) cc_final: 0.3910 (mmt) REVERT: T 26 HIS cc_start: 0.5346 (OUTLIER) cc_final: 0.5066 (t70) REVERT: Y 26 HIS cc_start: 0.5211 (OUTLIER) cc_final: 0.4988 (t70) REVERT: Z 19 MET cc_start: 0.4198 (tmm) cc_final: 0.3788 (mmt) REVERT: 1 19 MET cc_start: 0.4288 (tmm) cc_final: 0.3903 (mmt) REVERT: 1 26 HIS cc_start: 0.5334 (OUTLIER) cc_final: 0.5056 (t70) outliers start: 258 outliers final: 159 residues processed: 1081 average time/residue: 1.3046 time to fit residues: 1803.7255 Evaluate side-chains 1096 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 887 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 419 ILE Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 264 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 232 MET Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 419 ILE Chi-restraints excluded: chain R residue 26 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain Y residue 26 HIS Chi-restraints excluded: chain 1 residue 26 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 664 optimal weight: 0.9980 chunk 437 optimal weight: 9.9990 chunk 704 optimal weight: 3.9990 chunk 430 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 chunk 489 optimal weight: 0.0870 chunk 739 optimal weight: 0.6980 chunk 680 optimal weight: 0.9980 chunk 588 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 454 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN J 365 GLN K 365 GLN L 365 GLN M 365 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 56042 Z= 0.155 Angle : 0.544 11.078 75712 Z= 0.281 Chirality : 0.041 0.178 9142 Planarity : 0.003 0.032 9884 Dihedral : 4.236 57.087 7924 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.67 % Favored : 97.15 % Rotamer: Outliers : 3.83 % Allowed : 26.32 % Favored : 69.85 % 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: 1.81 (0.10), residues: 7462 helix: 2.37 (0.08), residues: 4228 sheet: -0.06 (0.16), residues: 1106 loop : -0.48 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP Q 23 HIS 0.001 0.000 HIS Z 26 PHE 0.013 0.001 PHE U 25 TYR 0.007 0.001 TYR F 505 ARG 0.005 0.000 ARG L 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 884 time to evaluate : 4.582 Fit side-chains REVERT: A 17 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: A 75 GLU cc_start: 0.7434 (tp30) cc_final: 0.7165 (tp30) REVERT: A 79 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7821 (ttpt) REVERT: A 213 GLU cc_start: 0.7252 (mp0) cc_final: 0.6759 (mp0) REVERT: A 224 LYS cc_start: 0.6176 (ttpp) cc_final: 0.5729 (pttp) REVERT: A 400 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.6944 (t-90) REVERT: A 403 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6697 (ttp-170) REVERT: A 444 ARG cc_start: 0.7980 (ttm170) cc_final: 0.6844 (tpt90) REVERT: A 483 GLU cc_start: 0.7196 (pt0) cc_final: 0.6990 (mt-10) REVERT: B 17 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6428 (tmt-80) REVERT: B 75 GLU cc_start: 0.7408 (tp30) cc_final: 0.6954 (tp30) REVERT: B 79 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7670 (ttpt) REVERT: B 224 LYS cc_start: 0.6346 (ttpp) cc_final: 0.5951 (pttp) REVERT: B 388 MET cc_start: 0.6020 (tpt) cc_final: 0.5659 (tpp) REVERT: B 400 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.6995 (t-90) REVERT: B 403 ARG cc_start: 0.7110 (ttm-80) cc_final: 0.6714 (ttp-170) REVERT: B 444 ARG cc_start: 0.8084 (ttm170) cc_final: 0.6841 (tpt90) REVERT: C 17 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6443 (tmt-80) REVERT: C 75 GLU cc_start: 0.7422 (tp30) cc_final: 0.7171 (tp30) REVERT: C 165 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6797 (mtt) REVERT: C 193 GLN cc_start: 0.7537 (pt0) cc_final: 0.7274 (pt0) REVERT: C 224 LYS cc_start: 0.6248 (ttpp) cc_final: 0.5726 (pttp) REVERT: C 283 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5926 (mpp80) REVERT: C 400 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.6919 (t-90) REVERT: D 12 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6274 (mtp180) REVERT: D 17 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6384 (tmt-80) REVERT: D 75 GLU cc_start: 0.7425 (tp30) cc_final: 0.6984 (tp30) REVERT: D 193 GLN cc_start: 0.7440 (pt0) cc_final: 0.7172 (pt0) REVERT: D 224 LYS cc_start: 0.6153 (ttpp) cc_final: 0.5815 (pttp) REVERT: D 400 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.7055 (t-90) REVERT: D 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6649 (ttp-110) REVERT: E 12 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6317 (mtp180) REVERT: E 17 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: E 75 GLU cc_start: 0.7447 (tp30) cc_final: 0.7021 (tp30) REVERT: E 224 LYS cc_start: 0.6032 (ttpp) cc_final: 0.5679 (pttp) REVERT: E 236 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5938 (mt) REVERT: E 283 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5826 (mpp80) REVERT: E 400 HIS cc_start: 0.7391 (OUTLIER) cc_final: 0.6957 (t-90) REVERT: F 12 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6234 (mtp180) REVERT: F 17 ARG cc_start: 0.7199 (ttp-110) cc_final: 0.6368 (tmt-80) REVERT: F 75 GLU cc_start: 0.7424 (tp30) cc_final: 0.6955 (tp30) REVERT: F 79 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7775 (ttpt) REVERT: F 193 GLN cc_start: 0.7503 (pt0) cc_final: 0.7239 (pt0) REVERT: F 224 LYS cc_start: 0.6282 (ttpp) cc_final: 0.5969 (pttp) REVERT: F 400 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6998 (t-90) REVERT: F 403 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6741 (ttp-170) REVERT: F 444 ARG cc_start: 0.7967 (ttm170) cc_final: 0.6770 (tpt90) REVERT: G 12 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.6532 (mtp180) REVERT: G 17 ARG cc_start: 0.7224 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: G 75 GLU cc_start: 0.7465 (tp30) cc_final: 0.6931 (tp30) REVERT: G 79 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7735 (ttpt) REVERT: G 224 LYS cc_start: 0.6221 (ttpp) cc_final: 0.5737 (pttp) REVERT: G 321 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.7049 (ttt-90) REVERT: G 400 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.7071 (t-90) REVERT: G 403 ARG cc_start: 0.7125 (ttm-80) cc_final: 0.6716 (ttp-170) REVERT: G 444 ARG cc_start: 0.8028 (ttm170) cc_final: 0.6776 (tpt90) REVERT: H 17 ARG cc_start: 0.7240 (ttp-110) cc_final: 0.6405 (tmt-80) REVERT: H 75 GLU cc_start: 0.7435 (tp30) cc_final: 0.7166 (tp30) REVERT: H 79 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7820 (ttpt) REVERT: H 224 LYS cc_start: 0.6177 (ttpp) cc_final: 0.5729 (pttp) REVERT: H 400 HIS cc_start: 0.7391 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: H 403 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6696 (ttp-170) REVERT: H 444 ARG cc_start: 0.7981 (ttm170) cc_final: 0.6843 (tpt90) REVERT: H 483 GLU cc_start: 0.7197 (pt0) cc_final: 0.6994 (mt-10) REVERT: I 12 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6322 (mtp180) REVERT: I 17 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6424 (tmt-80) REVERT: I 75 GLU cc_start: 0.7406 (tp30) cc_final: 0.6950 (tp30) REVERT: I 79 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7670 (ttpt) REVERT: I 224 LYS cc_start: 0.6314 (ttpp) cc_final: 0.5938 (pttp) REVERT: I 403 ARG cc_start: 0.7108 (ttm-80) cc_final: 0.6696 (ttp-170) REVERT: I 444 ARG cc_start: 0.8079 (ttm170) cc_final: 0.6842 (tpt90) REVERT: J 17 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6439 (tmt-80) REVERT: J 75 GLU cc_start: 0.7421 (tp30) cc_final: 0.7169 (tp30) REVERT: J 165 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6792 (mtt) REVERT: J 193 GLN cc_start: 0.7543 (pt0) cc_final: 0.7266 (pt0) REVERT: J 224 LYS cc_start: 0.6242 (ttpp) cc_final: 0.5727 (pttp) REVERT: J 283 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5923 (mpp80) REVERT: J 400 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.6923 (t-90) REVERT: K 12 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6272 (mtp180) REVERT: K 17 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6384 (tmt-80) REVERT: K 75 GLU cc_start: 0.7426 (tp30) cc_final: 0.6986 (tp30) REVERT: K 193 GLN cc_start: 0.7452 (pt0) cc_final: 0.7172 (pt0) REVERT: K 224 LYS cc_start: 0.6167 (ttpp) cc_final: 0.5749 (pttp) REVERT: K 400 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.7037 (t-90) REVERT: K 403 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6653 (ttp-110) REVERT: L 12 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6313 (mtp180) REVERT: L 17 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.6438 (tmt-80) REVERT: L 75 GLU cc_start: 0.7458 (tp30) cc_final: 0.7040 (tp30) REVERT: L 79 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7790 (ttpt) REVERT: L 193 GLN cc_start: 0.7437 (pt0) cc_final: 0.7201 (pt0) REVERT: L 224 LYS cc_start: 0.6101 (ttpp) cc_final: 0.5672 (pttp) REVERT: L 236 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5950 (mt) REVERT: L 283 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.5771 (mpp80) REVERT: L 400 HIS cc_start: 0.7404 (OUTLIER) cc_final: 0.6955 (t-90) REVERT: M 12 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6244 (mtp180) REVERT: M 17 ARG cc_start: 0.7201 (ttp-110) cc_final: 0.6370 (tmt-80) REVERT: M 75 GLU cc_start: 0.7423 (tp30) cc_final: 0.6954 (tp30) REVERT: M 79 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7779 (ttpt) REVERT: M 224 LYS cc_start: 0.6286 (ttpp) cc_final: 0.5970 (pttp) REVERT: M 388 MET cc_start: 0.5990 (tpt) cc_final: 0.5567 (tpp) REVERT: M 400 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6992 (t-90) REVERT: M 403 ARG cc_start: 0.7129 (ttm-80) cc_final: 0.6747 (ttp-170) REVERT: M 444 ARG cc_start: 0.7967 (ttm170) cc_final: 0.6770 (tpt90) REVERT: N 12 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6532 (mtp180) REVERT: N 17 ARG cc_start: 0.7224 (ttp-110) cc_final: 0.6441 (tmt-80) REVERT: N 75 GLU cc_start: 0.7469 (tp30) cc_final: 0.6930 (tp30) REVERT: N 79 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7733 (ttpt) REVERT: N 224 LYS cc_start: 0.6217 (ttpp) cc_final: 0.5748 (pttp) REVERT: N 400 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: N 403 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6713 (ttp-170) REVERT: N 444 ARG cc_start: 0.8028 (ttm170) cc_final: 0.6776 (tpt90) REVERT: S 19 MET cc_start: 0.4189 (tmm) cc_final: 0.3748 (mmt) REVERT: S 26 HIS cc_start: 0.5386 (OUTLIER) cc_final: 0.5137 (t70) REVERT: T 19 MET cc_start: 0.4270 (tmm) cc_final: 0.3920 (mmt) REVERT: T 26 HIS cc_start: 0.5246 (OUTLIER) cc_final: 0.4980 (t70) REVERT: Y 26 HIS cc_start: 0.5182 (OUTLIER) cc_final: 0.4972 (t70) REVERT: Z 19 MET cc_start: 0.4095 (tmm) cc_final: 0.3748 (mmt) REVERT: 1 19 MET cc_start: 0.4260 (tmm) cc_final: 0.3915 (mmt) REVERT: 1 26 HIS cc_start: 0.5254 (OUTLIER) cc_final: 0.4989 (t70) outliers start: 223 outliers final: 147 residues processed: 1051 average time/residue: 1.3010 time to fit residues: 1748.1274 Evaluate side-chains 1068 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 878 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 264 ASN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 60 GLU Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain J residue 419 ILE Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 288 LEU Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain L residue 419 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 232 MET Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 400 HIS Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 12 ARG Chi-restraints excluded: chain N residue 60 GLU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain S residue 26 HIS Chi-restraints excluded: chain T residue 26 HIS Chi-restraints excluded: chain Y residue 26 HIS Chi-restraints excluded: chain 1 residue 26 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 360 optimal weight: 0.9990 chunk 467 optimal weight: 2.9990 chunk 627 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 542 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 589 optimal weight: 6.9990 chunk 246 optimal weight: 0.0970 chunk 605 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN J 365 GLN K 365 GLN M 365 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.206901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126014 restraints weight = 54954.523| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.70 r_work: 0.3281 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 56042 Z= 0.247 Angle : 0.586 13.215 75712 Z= 0.302 Chirality : 0.043 0.188 9142 Planarity : 0.003 0.032 9884 Dihedral : 4.326 51.727 7924 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.67 % Favored : 97.15 % Rotamer: Outliers : 3.97 % Allowed : 26.24 % Favored : 69.80 % 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: 1.62 (0.10), residues: 7462 helix: 2.23 (0.08), residues: 4242 sheet: -0.20 (0.16), residues: 1106 loop : -0.57 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 23 HIS 0.003 0.002 HIS K 400 PHE 0.006 0.001 PHE G 194 TYR 0.011 0.001 TYR D 505 ARG 0.004 0.000 ARG L 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27874.51 seconds wall clock time: 474 minutes 6.25 seconds (28446.25 seconds total)