Starting phenix.real_space_refine on Fri Oct 11 11:05:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/10_2024/8s32_19687.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/10_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_19687/10_2024/8s32_19687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/10_2024/8s32_19687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/10_2024/8s32_19687.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s32_19687/10_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): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 11.28, 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: 11.19 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: 6.36 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: 23.91 Time building geometry restraints manager: 13.04 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: 6.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.740 Check model and map are aligned: 0.330 Set scattering table: 0.380 Process input model: 89.690 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 111.460 ------------------------------------------------------------------------------- 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 : 4.658 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: 1.5232 time to fit residues: 2729.2046 Evaluate side-chains 948 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 917 time to evaluate : 4.690 ------------------------------------------------------------------------------- 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: 0.1843 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= 0.257 Angle : 0.612 7.481 75712 Z= 0.319 Chirality : 0.044 0.201 9142 Planarity : 0.004 0.030 9884 Dihedral : 4.628 46.652 7959 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.09 % Favored : 97.72 % Rotamer: Outliers : 5.29 % Allowed : 24.97 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 1267 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 959 time to evaluate : 4.739 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: 0.7804 (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: 0.7955 (ttp80) cc_final: 0.6843 (tpt90) REVERT: A 483 GLU cc_start: 0.7294 (pt0) cc_final: 0.7021 (mt-10) REVERT: B 17 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6436 (tmt-80) REVERT: B 75 GLU cc_start: 0.7380 (tp30) cc_final: 0.6897 (tp30) REVERT: B 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7764 (ttpt) REVERT: B 110 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.6768 (mtm) REVERT: B 184 ASP cc_start: 0.6718 (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: 0.6579 (mp0) REVERT: B 224 LYS cc_start: 0.6211 (ttpp) cc_final: 0.5752 (pttp) REVERT: B 397 ASP cc_start: 0.6811 (m-30) cc_final: 0.6517 (t0) REVERT: B 403 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6771 (ttp-170) REVERT: C 17 ARG cc_start: 0.7253 (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: 0.7402 (OUTLIER) cc_final: 0.6970 (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: 0.6168 (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 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: 0.7994 (OUTLIER) cc_final: 0.7772 (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: 0.6139 (ttpp) cc_final: 0.5779 (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: 0.6406 (tmt-80) REVERT: F 75 GLU cc_start: 0.7442 (tp30) cc_final: 0.6934 (tp30) REVERT: F 79 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7783 (ttpt) REVERT: F 193 GLN cc_start: 0.7545 (pt0) cc_final: 0.7285 (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: 0.7084 (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: 0.7397 (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: 0.6819 (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: 0.7398 (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: 0.7382 (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: 0.8723 (OUTLIER) cc_final: 0.6720 (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 380 VAL cc_start: 0.7900 (m) cc_final: 0.7658 (m) 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: 0.7783 (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: 0.6573 (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: 0.6594 (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: 0.7403 (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: 0.6429 (m-30) REVERT: K 192 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7005 (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: 0.8153 (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: 0.7998 (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: 0.7103 (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: 0.6322 (mtp180) REVERT: M 17 ARG cc_start: 0.7214 (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: 0.7531 (pt0) cc_final: 0.7254 (pt0) REVERT: M 213 GLU cc_start: 0.7107 (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: 0.7161 (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: 0.7890 (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: 0.7216 (ttp-110) cc_final: 0.6472 (tmt-80) REVERT: N 75 GLU cc_start: 0.7402 (tp30) cc_final: 0.6870 (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: 0.7321 (pt0) REVERT: N 224 LYS cc_start: 0.6090 (ttpp) cc_final: 0.5702 (pttp) REVERT: N 264 ASN cc_start: 0.6134 (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: 0.7044 (ttm-80) cc_final: 0.6727 (ttp-170) outliers start: 308 outliers final: 103 residues processed: 1154 average time/residue: 1.4090 time to fit residues: 2033.9451 Evaluate side-chains 1032 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 879 time to evaluate : 4.623 ------------------------------------------------------------------------------- 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 153 SER 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: 1.9990 chunk 209 optimal weight: 0.9990 chunk 560 optimal weight: 4.9990 chunk 458 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 675 optimal weight: 1.9990 chunk 729 optimal weight: 6.9990 chunk 601 optimal weight: 5.9990 chunk 669 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 541 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 56042 Z= 0.205 Angle : 0.545 7.805 75712 Z= 0.286 Chirality : 0.042 0.154 9142 Planarity : 0.003 0.028 9884 Dihedral : 4.512 44.287 7946 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.59 % Favored : 97.23 % Rotamer: Outliers : 5.17 % Allowed : 23.92 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.10), residues: 7462 helix: 2.21 (0.08), residues: 4228 sheet: -0.22 (0.15), residues: 1106 loop : -0.36 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 2 23 HIS 0.003 0.001 HIS E 400 PHE 0.006 0.001 PHE G 194 TYR 0.011 0.001 TYR C 505 ARG 0.004 0.000 ARG B 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 1186 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 885 time to evaluate : 4.792 Fit side-chains REVERT: A 17 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6409 (tmt-80) REVERT: A 75 GLU cc_start: 0.7435 (tp30) cc_final: 0.6928 (tp30) REVERT: A 79 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7762 (ttpt) REVERT: A 184 ASP cc_start: 0.6829 (m-30) cc_final: 0.6474 (m-30) REVERT: A 213 GLU cc_start: 0.7135 (mp0) cc_final: 0.6712 (mp0) REVERT: A 224 LYS cc_start: 0.6173 (ttpp) cc_final: 0.5817 (pttp) REVERT: A 397 ASP cc_start: 0.6844 (m-30) cc_final: 0.6588 (t0) REVERT: A 400 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6923 (t-90) REVERT: A 403 ARG cc_start: 0.7069 (ttm-80) cc_final: 0.6737 (ttp-170) REVERT: A 444 ARG cc_start: 0.7931 (ttp80) cc_final: 0.6829 (tpt90) REVERT: A 483 GLU cc_start: 0.7226 (pt0) cc_final: 0.6967 (mt-10) REVERT: B 17 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.6449 (tmt-80) REVERT: B 75 GLU cc_start: 0.7425 (tp30) cc_final: 0.6943 (tp30) REVERT: B 79 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7609 (mtmm) REVERT: B 213 GLU cc_start: 0.7038 (mp0) cc_final: 0.6572 (mp0) REVERT: B 224 LYS cc_start: 0.6176 (ttpp) cc_final: 0.5771 (pttp) REVERT: B 400 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6952 (t-90) REVERT: B 403 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6764 (ttp-170) REVERT: C 12 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6266 (mtp180) REVERT: C 17 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6443 (tmt-80) REVERT: C 75 GLU cc_start: 0.7429 (tp30) cc_final: 0.7091 (tp30) REVERT: C 79 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7756 (ttpt) REVERT: C 165 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6955 (mtt) REVERT: C 213 GLU cc_start: 0.7063 (mp0) cc_final: 0.6647 (mp0) REVERT: C 224 LYS cc_start: 0.6201 (ttpp) cc_final: 0.5700 (pttp) REVERT: C 400 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.6967 (t-90) REVERT: D 12 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6326 (mtp180) REVERT: D 17 ARG cc_start: 0.7198 (ttp-110) cc_final: 0.6393 (tmt-80) REVERT: D 75 GLU cc_start: 0.7460 (tp30) cc_final: 0.7024 (tp30) REVERT: D 79 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7747 (ttpt) REVERT: D 165 MET cc_start: 0.7365 (mtm) cc_final: 0.7160 (mtt) REVERT: D 224 LYS cc_start: 0.6238 (ttpp) cc_final: 0.5725 (pttp) REVERT: D 397 ASP cc_start: 0.6876 (m-30) cc_final: 0.6563 (t0) REVERT: D 400 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6999 (t-90) REVERT: D 403 ARG cc_start: 0.7147 (ttm-80) cc_final: 0.6774 (ttp-170) REVERT: E 12 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.6396 (mtp180) REVERT: E 17 ARG cc_start: 0.7276 (ttp-110) cc_final: 0.6471 (tmt-80) REVERT: E 75 GLU cc_start: 0.7503 (tp30) cc_final: 0.6997 (tp30) REVERT: E 79 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7714 (ttpt) REVERT: E 184 ASP cc_start: 0.6765 (m-30) cc_final: 0.6485 (m-30) REVERT: E 190 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7212 (mm-30) REVERT: E 193 GLN cc_start: 0.7503 (pt0) cc_final: 0.7295 (pt0) REVERT: E 213 GLU cc_start: 0.7088 (mp0) cc_final: 0.6636 (mp0) REVERT: E 224 LYS cc_start: 0.6065 (ttpp) cc_final: 0.5607 (pttp) REVERT: E 379 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7593 (mmtt) REVERT: E 397 ASP cc_start: 0.6785 (m-30) cc_final: 0.6525 (t0) REVERT: E 400 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6953 (t-90) REVERT: F 12 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.6303 (mtp180) REVERT: F 17 ARG cc_start: 0.7204 (ttp-110) cc_final: 0.6389 (tmt-80) REVERT: F 75 GLU cc_start: 0.7480 (tp30) cc_final: 0.6964 (tp30) REVERT: F 79 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7764 (ttpt) REVERT: F 213 GLU cc_start: 0.7170 (mp0) cc_final: 0.6624 (mp0) REVERT: F 224 LYS cc_start: 0.6168 (ttpp) cc_final: 0.5851 (pttp) REVERT: F 397 ASP cc_start: 0.6812 (m-30) cc_final: 0.6545 (t0) REVERT: F 400 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.7009 (t-90) REVERT: F 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6795 (ttp-170) REVERT: F 444 ARG cc_start: 0.7891 (ttp80) cc_final: 0.6725 (tpt90) REVERT: G 12 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6614 (mtp180) REVERT: G 17 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6455 (tmt-80) REVERT: G 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6908 (tp30) REVERT: G 79 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7746 (ttpt) REVERT: G 165 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7035 (mtt) REVERT: G 224 LYS cc_start: 0.6162 (ttpp) cc_final: 0.5738 (pttp) REVERT: G 264 ASN cc_start: 0.6189 (OUTLIER) cc_final: 0.5980 (m-40) REVERT: G 397 ASP cc_start: 0.6802 (m-30) cc_final: 0.6520 (t0) REVERT: G 400 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7068 (t-90) REVERT: G 403 ARG cc_start: 0.7058 (ttm-80) cc_final: 0.6711 (ttp-170) REVERT: H 17 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6411 (tmt-80) REVERT: H 75 GLU cc_start: 0.7440 (tp30) cc_final: 0.6932 (tp30) REVERT: H 79 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7761 (ttpt) REVERT: H 184 ASP cc_start: 0.6832 (m-30) cc_final: 0.6477 (m-30) REVERT: H 213 GLU cc_start: 0.7146 (mp0) cc_final: 0.6707 (mp0) REVERT: H 224 LYS cc_start: 0.6173 (ttpp) cc_final: 0.5824 (pttp) REVERT: H 397 ASP cc_start: 0.6840 (m-30) cc_final: 0.6587 (t0) REVERT: H 400 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6923 (t-90) REVERT: H 403 ARG cc_start: 0.7072 (ttm-80) cc_final: 0.6737 (ttp-170) REVERT: H 444 ARG cc_start: 0.7933 (ttp80) cc_final: 0.6830 (tpt90) REVERT: H 483 GLU cc_start: 0.7227 (pt0) cc_final: 0.6969 (mt-10) REVERT: I 12 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6383 (mtp180) REVERT: I 17 ARG cc_start: 0.7249 (ttp-110) cc_final: 0.6446 (tmt-80) REVERT: I 75 GLU cc_start: 0.7437 (tp30) cc_final: 0.6953 (tp30) REVERT: I 79 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7608 (mtmm) REVERT: I 213 GLU cc_start: 0.7022 (mp0) cc_final: 0.6565 (mp0) REVERT: I 224 LYS cc_start: 0.6183 (ttpp) cc_final: 0.5785 (pttp) REVERT: I 400 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6949 (t-90) REVERT: I 403 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6756 (ttp-170) REVERT: J 12 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6266 (mtp180) REVERT: J 17 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: J 75 GLU cc_start: 0.7421 (tp30) cc_final: 0.7082 (tp30) REVERT: J 79 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7783 (ttpt) REVERT: J 165 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6960 (mtt) REVERT: J 213 GLU cc_start: 0.7087 (mp0) cc_final: 0.6634 (mp0) REVERT: J 224 LYS cc_start: 0.6198 (ttpp) cc_final: 0.5760 (pttp) REVERT: J 400 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6958 (t-90) REVERT: K 12 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6324 (mtp180) REVERT: K 17 ARG cc_start: 0.7201 (ttp-110) cc_final: 0.6392 (tmt-80) REVERT: K 75 GLU cc_start: 0.7456 (tp30) cc_final: 0.7021 (tp30) REVERT: K 79 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7748 (ttpt) REVERT: K 213 GLU cc_start: 0.7155 (mp0) cc_final: 0.6710 (mp0) REVERT: K 224 LYS cc_start: 0.6216 (ttpp) cc_final: 0.5694 (pttp) REVERT: K 397 ASP cc_start: 0.6861 (m-30) cc_final: 0.6555 (t0) REVERT: K 400 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.7007 (t-90) REVERT: K 403 ARG cc_start: 0.7139 (ttm-80) cc_final: 0.6769 (ttp-170) REVERT: L 12 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6394 (mtp180) REVERT: L 17 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6468 (tmt-80) REVERT: L 75 GLU cc_start: 0.7494 (tp30) cc_final: 0.6993 (tp30) REVERT: L 79 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7747 (ttpt) REVERT: L 184 ASP cc_start: 0.6764 (m-30) cc_final: 0.6486 (m-30) REVERT: L 190 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7206 (mm-30) REVERT: L 224 LYS cc_start: 0.6102 (ttpp) cc_final: 0.5751 (pttp) REVERT: L 397 ASP cc_start: 0.6781 (m-30) cc_final: 0.6518 (t0) REVERT: L 400 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: M 12 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.6300 (mtp180) REVERT: M 17 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6400 (tmt-80) REVERT: M 75 GLU cc_start: 0.7473 (tp30) cc_final: 0.6955 (tp30) REVERT: M 79 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7757 (ttpt) REVERT: M 224 LYS cc_start: 0.6166 (ttpp) cc_final: 0.5841 (pttp) REVERT: M 397 ASP cc_start: 0.6811 (m-30) cc_final: 0.6543 (t0) REVERT: M 400 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.7018 (t-90) REVERT: M 403 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6729 (ttp-170) REVERT: M 444 ARG cc_start: 0.7899 (ttp80) cc_final: 0.6730 (tpt90) REVERT: M 483 GLU cc_start: 0.7220 (pt0) cc_final: 0.6973 (mt-10) REVERT: N 12 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6610 (mtp180) REVERT: N 17 ARG cc_start: 0.7220 (ttp-110) cc_final: 0.6458 (tmt-80) REVERT: N 75 GLU cc_start: 0.7436 (tp30) cc_final: 0.6905 (tp30) REVERT: N 79 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7721 (ttpt) REVERT: N 165 MET cc_start: 0.7309 (mtp) cc_final: 0.7091 (mtt) REVERT: N 224 LYS cc_start: 0.6124 (ttpp) cc_final: 0.5606 (pttp) REVERT: N 320 LYS cc_start: 0.7183 (tptt) cc_final: 0.6901 (tppt) REVERT: N 397 ASP cc_start: 0.6783 (m-30) cc_final: 0.6526 (t0) REVERT: N 400 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.7058 (t-90) REVERT: N 403 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6732 (ttp-170) outliers start: 301 outliers final: 147 residues processed: 1087 average time/residue: 1.3502 time to fit residues: 1855.3488 Evaluate side-chains 1050 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 860 time to evaluate : 4.714 ------------------------------------------------------------------------------- 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 176 VAL 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 153 SER 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 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 165 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 275 VAL 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 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 176 VAL 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 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 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 ASP 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 386 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 176 VAL 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 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 153 SER Chi-restraints excluded: chain G residue 165 MET 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 176 VAL 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 153 SER 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 I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain J residue 12 ARG 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 178 ASP Chi-restraints excluded: chain J residue 186 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 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 79 LYS Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER 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 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 178 ASP 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 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 178 ASP 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 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 153 SER Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 276 LYS 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 386 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: 0.5980 chunk 507 optimal weight: 5.9990 chunk 350 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 322 optimal weight: 1.9990 chunk 453 optimal weight: 6.9990 chunk 677 optimal weight: 0.8980 chunk 717 optimal weight: 0.9980 chunk 353 optimal weight: 0.5980 chunk 642 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN B 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN H 365 GLN I 365 GLN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2420 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= 0.158 Angle : 0.516 7.402 75712 Z= 0.271 Chirality : 0.041 0.152 9142 Planarity : 0.003 0.028 9884 Dihedral : 4.474 52.043 7940 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.87 % Favored : 96.94 % Rotamer: Outliers : 5.07 % Allowed : 24.07 % Favored : 70.86 % 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: 1.78 (0.10), residues: 7462 helix: 2.31 (0.08), residues: 4228 sheet: -0.18 (0.16), residues: 1106 loop : -0.34 (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 0.008 0.001 PHE G 194 TYR 0.011 0.001 TYR K 505 ARG 0.004 0.000 ARG I 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 1185 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 890 time to evaluate : 4.802 Fit side-chains REVERT: A 17 ARG cc_start: 0.7237 (ttp-110) cc_final: 0.6410 (tmt-80) REVERT: A 75 GLU cc_start: 0.7386 (tp30) cc_final: 0.6892 (tp30) REVERT: A 79 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7791 (ttpt) REVERT: A 213 GLU cc_start: 0.7189 (mp0) cc_final: 0.6693 (mp0) REVERT: A 224 LYS cc_start: 0.6208 (ttpp) cc_final: 0.5788 (pttp) REVERT: A 397 ASP cc_start: 0.6821 (m-30) cc_final: 0.6546 (t0) REVERT: A 400 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6957 (t-90) REVERT: A 403 ARG cc_start: 0.7056 (ttm-80) cc_final: 0.6714 (ttp-170) REVERT: A 444 ARG cc_start: 0.7922 (ttp80) cc_final: 0.6835 (tpt90) REVERT: A 483 GLU cc_start: 0.7219 (pt0) cc_final: 0.6980 (mt-10) REVERT: B 17 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6417 (tmt-80) REVERT: B 75 GLU cc_start: 0.7427 (tp30) cc_final: 0.6922 (tp30) REVERT: B 79 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7702 (ttpt) REVERT: B 213 GLU cc_start: 0.7089 (mp0) cc_final: 0.6625 (mp0) REVERT: B 224 LYS cc_start: 0.6137 (ttpp) cc_final: 0.5832 (pttp) REVERT: B 400 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6960 (t-90) REVERT: B 403 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6770 (ttp-170) REVERT: C 17 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6422 (tmt-80) REVERT: C 75 GLU cc_start: 0.7428 (tp30) cc_final: 0.7083 (tp30) REVERT: C 79 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7780 (ttpt) REVERT: C 165 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6855 (mtt) REVERT: C 213 GLU cc_start: 0.7060 (mp0) cc_final: 0.6628 (mp0) REVERT: C 224 LYS cc_start: 0.6214 (ttpp) cc_final: 0.5777 (pttp) REVERT: C 236 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5977 (mt) REVERT: C 400 HIS cc_start: 0.7336 (OUTLIER) cc_final: 0.6958 (t-90) REVERT: D 12 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6294 (mtp180) REVERT: D 17 ARG cc_start: 0.7179 (ttp-110) cc_final: 0.6367 (tmt-80) REVERT: D 75 GLU cc_start: 0.7440 (tp30) cc_final: 0.6992 (tp30) REVERT: D 79 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7770 (ttpt) REVERT: D 213 GLU cc_start: 0.7151 (mp0) cc_final: 0.6662 (mp0) REVERT: D 224 LYS cc_start: 0.6181 (ttpp) cc_final: 0.5710 (pttp) REVERT: D 400 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.7034 (t-90) REVERT: D 403 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6751 (ttp-170) REVERT: E 12 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6369 (mtp180) REVERT: E 17 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.6436 (tmt-80) REVERT: E 75 GLU cc_start: 0.7448 (tp30) cc_final: 0.6978 (tp30) REVERT: E 79 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7749 (ttpt) REVERT: E 213 GLU cc_start: 0.7107 (mp0) cc_final: 0.6690 (mp0) REVERT: E 224 LYS cc_start: 0.6058 (ttpp) cc_final: 0.5690 (pttp) REVERT: E 236 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5893 (mt) REVERT: E 283 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.5796 (mpp80) REVERT: E 397 ASP cc_start: 0.6774 (m-30) cc_final: 0.6497 (t0) REVERT: E 400 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6983 (t-90) REVERT: F 12 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6268 (mtp180) REVERT: F 17 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.6394 (tmt-80) REVERT: F 75 GLU cc_start: 0.7458 (tp30) cc_final: 0.6979 (tp30) REVERT: F 79 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7775 (ttpt) REVERT: F 213 GLU cc_start: 0.7203 (mp0) cc_final: 0.6691 (mp0) REVERT: F 224 LYS cc_start: 0.6231 (ttpp) cc_final: 0.5824 (pttp) REVERT: F 397 ASP cc_start: 0.6811 (m-30) cc_final: 0.6530 (t0) REVERT: F 400 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.7015 (t-90) REVERT: F 403 ARG cc_start: 0.7040 (ttm-80) cc_final: 0.6649 (ttp-170) REVERT: F 444 ARG cc_start: 0.7893 (ttp80) cc_final: 0.6734 (tpt90) REVERT: G 12 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6580 (mtp180) REVERT: G 17 ARG cc_start: 0.7206 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: G 75 GLU cc_start: 0.7436 (tp30) cc_final: 0.6890 (tp30) REVERT: G 79 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7754 (ttpt) REVERT: G 165 MET cc_start: 0.7283 (mtm) cc_final: 0.6990 (mtt) REVERT: G 213 GLU cc_start: 0.7156 (mp0) cc_final: 0.6655 (mp0) REVERT: G 224 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5808 (pttp) REVERT: G 397 ASP cc_start: 0.6821 (m-30) cc_final: 0.6533 (t0) REVERT: G 400 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.7050 (t-90) REVERT: G 403 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.6707 (ttp-170) REVERT: H 17 ARG cc_start: 0.7231 (ttp-110) cc_final: 0.6408 (tmt-80) REVERT: H 75 GLU cc_start: 0.7388 (tp30) cc_final: 0.6892 (tp30) REVERT: H 79 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7788 (ttpt) REVERT: H 213 GLU cc_start: 0.7162 (mp0) cc_final: 0.6682 (mp0) REVERT: H 224 LYS cc_start: 0.6205 (ttpp) cc_final: 0.5785 (pttp) REVERT: H 397 ASP cc_start: 0.6818 (m-30) cc_final: 0.6543 (t0) REVERT: H 400 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6957 (t-90) REVERT: H 403 ARG cc_start: 0.7056 (ttm-80) cc_final: 0.6713 (ttp-170) REVERT: H 444 ARG cc_start: 0.7926 (ttp80) cc_final: 0.6844 (tpt90) REVERT: H 483 GLU cc_start: 0.7222 (pt0) cc_final: 0.6985 (mt-10) REVERT: I 12 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6349 (mtp180) REVERT: I 17 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6416 (tmt-80) REVERT: I 75 GLU cc_start: 0.7427 (tp30) cc_final: 0.6921 (tp30) REVERT: I 79 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7708 (ttpt) REVERT: I 224 LYS cc_start: 0.6170 (ttpp) cc_final: 0.5780 (pttp) REVERT: I 400 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.6950 (t-90) REVERT: I 403 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6773 (ttp-170) REVERT: J 17 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6418 (tmt-80) REVERT: J 75 GLU cc_start: 0.7428 (tp30) cc_final: 0.7085 (tp30) REVERT: J 79 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7782 (ttpt) REVERT: J 165 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6842 (mtt) REVERT: J 193 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: J 213 GLU cc_start: 0.7083 (mp0) cc_final: 0.6674 (mp0) REVERT: J 224 LYS cc_start: 0.6195 (ttpp) cc_final: 0.5770 (pttp) REVERT: J 236 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5972 (mt) REVERT: J 400 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: K 12 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6295 (mtp180) REVERT: K 17 ARG cc_start: 0.7175 (ttp-110) cc_final: 0.6363 (tmt-80) REVERT: K 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6992 (tp30) REVERT: K 79 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7768 (ttpt) REVERT: K 213 GLU cc_start: 0.7168 (mp0) cc_final: 0.6729 (mp0) REVERT: K 224 LYS cc_start: 0.6200 (ttpp) cc_final: 0.5719 (pttp) REVERT: K 400 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.7034 (t-90) REVERT: K 403 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6739 (ttp-170) REVERT: L 12 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6367 (mtp180) REVERT: L 17 ARG cc_start: 0.7264 (ttp-110) cc_final: 0.6433 (tmt-80) REVERT: L 75 GLU cc_start: 0.7446 (tp30) cc_final: 0.6975 (tp30) REVERT: L 79 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7756 (ttpt) REVERT: L 213 GLU cc_start: 0.7162 (mp0) cc_final: 0.6760 (mp0) REVERT: L 224 LYS cc_start: 0.6055 (ttpp) cc_final: 0.5660 (pttp) REVERT: L 236 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5945 (mt) REVERT: L 283 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.5769 (mpp80) REVERT: L 397 ASP cc_start: 0.6798 (m-30) cc_final: 0.6521 (t0) REVERT: L 400 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6967 (t-90) REVERT: M 12 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6271 (mtp180) REVERT: M 17 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: M 75 GLU cc_start: 0.7451 (tp30) cc_final: 0.6969 (tp30) REVERT: M 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7775 (ttpt) REVERT: M 213 GLU cc_start: 0.7196 (mp0) cc_final: 0.6663 (mp0) REVERT: M 224 LYS cc_start: 0.6237 (ttpp) cc_final: 0.5823 (pttp) REVERT: M 400 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.7012 (t-90) REVERT: M 403 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6688 (ttp-170) REVERT: M 444 ARG cc_start: 0.7898 (ttp80) cc_final: 0.6741 (tpt90) REVERT: M 483 GLU cc_start: 0.7183 (pt0) cc_final: 0.6932 (mt-10) REVERT: N 12 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6579 (mtp180) REVERT: N 17 ARG cc_start: 0.7206 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: N 75 GLU cc_start: 0.7432 (tp30) cc_final: 0.6886 (tp30) REVERT: N 79 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7746 (ttpt) REVERT: N 165 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7056 (mtt) REVERT: N 213 GLU cc_start: 0.7180 (mp0) cc_final: 0.6723 (mp0) REVERT: N 224 LYS cc_start: 0.6102 (ttpp) cc_final: 0.5689 (pttp) REVERT: N 236 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.6002 (mt) REVERT: N 320 LYS cc_start: 0.7211 (tptt) cc_final: 0.6898 (tppt) REVERT: N 397 ASP cc_start: 0.6829 (m-30) cc_final: 0.6546 (t0) REVERT: N 400 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.7067 (t-90) REVERT: N 403 ARG cc_start: 0.7074 (ttm-80) cc_final: 0.6710 (ttp-170) REVERT: T 26 HIS cc_start: 0.5240 (OUTLIER) cc_final: 0.5018 (t70) REVERT: Y 26 HIS cc_start: 0.5202 (OUTLIER) cc_final: 0.4988 (t70) REVERT: 1 26 HIS cc_start: 0.5212 (OUTLIER) cc_final: 0.4990 (t70) outliers start: 295 outliers final: 120 residues processed: 1105 average time/residue: 1.3379 time to fit residues: 1871.9069 Evaluate side-chains 1045 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 874 time to evaluate : 4.677 ------------------------------------------------------------------------------- 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 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 86 ASP 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 400 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET 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 329 THR 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 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 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 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 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 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 320 LYS 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 186 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 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 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 86 ASP Chi-restraints excluded: chain I residue 186 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 368 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 165 MET Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 193 GLN 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 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 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 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 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU 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 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 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 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 165 MET Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 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 400 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 1 residue 26 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 597 optimal weight: 20.0000 chunk 407 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 534 optimal weight: 4.9990 chunk 295 optimal weight: 20.0000 chunk 612 optimal weight: 1.9990 chunk 495 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 chunk 643 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN K 365 GLN L 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 56042 Z= 0.336 Angle : 0.608 8.414 75712 Z= 0.317 Chirality : 0.045 0.153 9142 Planarity : 0.004 0.032 9884 Dihedral : 4.840 59.552 7932 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 6.59 % Allowed : 22.75 % Favored : 70.66 % 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: 1.27 (0.09), residues: 7462 helix: 1.98 (0.08), residues: 4228 sheet: -0.63 (0.17), residues: 966 loop : -0.61 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 23 HIS 0.005 0.002 HIS B 400 PHE 0.006 0.001 PHE U 25 TYR 0.015 0.001 TYR K 505 ARG 0.004 0.001 ARG E 12 *********************** 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 1264 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 880 time to evaluate : 4.721 Fit side-chains REVERT: A 17 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6421 (tmt-80) REVERT: A 75 GLU cc_start: 0.7475 (tp30) cc_final: 0.7039 (tp30) REVERT: A 79 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7735 (ttpt) REVERT: A 184 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: A 213 GLU cc_start: 0.7163 (mp0) cc_final: 0.6652 (mp0) REVERT: A 224 LYS cc_start: 0.6232 (ttpp) cc_final: 0.5849 (pttp) REVERT: A 306 MET cc_start: 0.4346 (mmp) cc_final: 0.4090 (mmp) REVERT: A 400 HIS cc_start: 0.7404 (OUTLIER) cc_final: 0.6868 (t-90) REVERT: A 403 ARG cc_start: 0.7055 (ttm-80) cc_final: 0.6653 (ttp-170) REVERT: A 483 GLU cc_start: 0.7269 (pt0) cc_final: 0.7012 (mt-10) REVERT: B 17 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.6464 (tmt-80) REVERT: B 75 GLU cc_start: 0.7445 (tp30) cc_final: 0.6972 (tp30) REVERT: B 79 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7585 (mtmm) REVERT: B 184 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6766 (m-30) REVERT: B 224 LYS cc_start: 0.6098 (ttpp) cc_final: 0.5754 (pttp) REVERT: B 366 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: B 400 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: B 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6683 (ttp-170) REVERT: C 17 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.6487 (tmt-80) REVERT: C 75 GLU cc_start: 0.7466 (tp30) cc_final: 0.7032 (tp30) REVERT: C 79 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7612 (mtmm) REVERT: C 165 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6754 (mtt) REVERT: C 184 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6754 (m-30) REVERT: C 193 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: C 213 GLU cc_start: 0.7030 (mp0) cc_final: 0.6576 (mp0) REVERT: C 224 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5739 (pttp) REVERT: C 236 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5996 (mt) REVERT: C 306 MET cc_start: 0.4333 (mmp) cc_final: 0.4077 (mmp) REVERT: C 400 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.6914 (t-90) REVERT: D 12 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6268 (mtp180) REVERT: D 17 ARG cc_start: 0.7269 (ttp-110) cc_final: 0.6454 (tmt-80) REVERT: D 75 GLU cc_start: 0.7494 (tp30) cc_final: 0.7045 (tp30) REVERT: D 79 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7721 (ttpt) REVERT: D 184 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6834 (m-30) REVERT: D 193 GLN cc_start: 0.7386 (pt0) cc_final: 0.7018 (pt0) REVERT: D 213 GLU cc_start: 0.7044 (mp0) cc_final: 0.6560 (mp0) REVERT: D 224 LYS cc_start: 0.6191 (ttpp) cc_final: 0.5711 (pttp) REVERT: D 306 MET cc_start: 0.4506 (mmp) cc_final: 0.4256 (mmp) REVERT: D 400 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: D 403 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6616 (ttp-110) REVERT: E 12 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.6403 (mtp180) REVERT: E 17 ARG cc_start: 0.7316 (ttp-110) cc_final: 0.6482 (tmt-80) REVERT: E 43 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6701 (p90) REVERT: E 75 GLU cc_start: 0.7523 (tp30) cc_final: 0.7036 (tp30) REVERT: E 79 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7723 (ttpt) REVERT: E 184 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: E 224 LYS cc_start: 0.6042 (ttpp) cc_final: 0.5660 (pttp) REVERT: E 236 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5915 (mt) REVERT: E 283 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.5871 (mpp80) REVERT: E 306 MET cc_start: 0.4614 (mmp) cc_final: 0.4353 (mmp) REVERT: E 321 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6390 (ttt-90) REVERT: E 400 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.6890 (t-90) REVERT: F 12 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6277 (mtp180) REVERT: F 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6429 (tmt-80) REVERT: F 75 GLU cc_start: 0.7489 (tp30) cc_final: 0.7030 (tp30) REVERT: F 184 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6642 (m-30) REVERT: F 213 GLU cc_start: 0.7147 (mp0) cc_final: 0.6578 (mp0) REVERT: F 224 LYS cc_start: 0.6220 (ttpp) cc_final: 0.5802 (pttp) REVERT: F 264 ASN cc_start: 0.6017 (OUTLIER) cc_final: 0.5700 (t0) REVERT: F 400 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6916 (t-90) REVERT: F 403 ARG cc_start: 0.7093 (ttm-80) cc_final: 0.6842 (mtt-85) REVERT: G 12 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.6500 (mtp180) REVERT: G 17 ARG cc_start: 0.7281 (ttp-110) cc_final: 0.6495 (tmt-80) REVERT: G 75 GLU cc_start: 0.7461 (tp30) cc_final: 0.6934 (tp30) REVERT: G 79 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7709 (ttpt) REVERT: G 165 MET cc_start: 0.7256 (mtp) cc_final: 0.7055 (mtt) REVERT: G 184 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6763 (m-30) REVERT: G 224 LYS cc_start: 0.6123 (ttpp) cc_final: 0.5753 (pttp) REVERT: G 264 ASN cc_start: 0.6171 (OUTLIER) cc_final: 0.5914 (m-40) REVERT: G 306 MET cc_start: 0.4245 (mmp) cc_final: 0.4021 (mmp) REVERT: G 400 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7019 (t-90) REVERT: G 403 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6689 (ttp-170) REVERT: H 17 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6420 (tmt-80) REVERT: H 75 GLU cc_start: 0.7476 (tp30) cc_final: 0.7039 (tp30) REVERT: H 79 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7734 (ttpt) REVERT: H 184 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6725 (m-30) REVERT: H 213 GLU cc_start: 0.7141 (mp0) cc_final: 0.6629 (mp0) REVERT: H 224 LYS cc_start: 0.6226 (ttpp) cc_final: 0.5846 (pttp) REVERT: H 306 MET cc_start: 0.4336 (mmp) cc_final: 0.4078 (mmp) REVERT: H 400 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6866 (t-90) REVERT: H 403 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.6649 (ttp-170) REVERT: H 483 GLU cc_start: 0.7269 (pt0) cc_final: 0.7015 (mt-10) REVERT: I 12 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6272 (mtp180) REVERT: I 17 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6463 (tmt-80) REVERT: I 75 GLU cc_start: 0.7446 (tp30) cc_final: 0.6971 (tp30) REVERT: I 79 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7584 (mtmm) REVERT: I 184 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6766 (m-30) REVERT: I 224 LYS cc_start: 0.6127 (ttpp) cc_final: 0.5790 (pttp) REVERT: I 400 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6905 (t-90) REVERT: I 403 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6682 (ttp-170) REVERT: J 17 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.6484 (tmt-80) REVERT: J 75 GLU cc_start: 0.7468 (tp30) cc_final: 0.7033 (tp30) REVERT: J 79 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7604 (mtmm) REVERT: J 165 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6761 (mtt) REVERT: J 184 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: J 213 GLU cc_start: 0.7035 (mp0) cc_final: 0.6521 (mp0) REVERT: J 224 LYS cc_start: 0.6187 (ttpp) cc_final: 0.5757 (pttp) REVERT: J 236 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5987 (mt) REVERT: J 306 MET cc_start: 0.4372 (mmp) cc_final: 0.4111 (mmp) REVERT: J 400 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6918 (t-90) REVERT: K 12 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6268 (mtp180) REVERT: K 17 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.6452 (tmt-80) REVERT: K 75 GLU cc_start: 0.7494 (tp30) cc_final: 0.7047 (tp30) REVERT: K 79 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7721 (ttpt) REVERT: K 184 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6853 (m-30) REVERT: K 193 GLN cc_start: 0.7411 (pt0) cc_final: 0.7033 (pt0) REVERT: K 213 GLU cc_start: 0.7140 (mp0) cc_final: 0.6634 (mp0) REVERT: K 224 LYS cc_start: 0.6193 (ttpp) cc_final: 0.5709 (pttp) REVERT: K 306 MET cc_start: 0.4538 (mmp) cc_final: 0.4284 (mmp) REVERT: K 400 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.6976 (t-90) REVERT: K 403 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6613 (ttp-110) REVERT: L 12 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.6400 (mtp180) REVERT: L 17 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.6486 (tmt-80) REVERT: L 43 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6705 (p90) REVERT: L 75 GLU cc_start: 0.7518 (tp30) cc_final: 0.7037 (tp30) REVERT: L 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7590 (mtmm) REVERT: L 184 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: L 193 GLN cc_start: 0.7471 (pt0) cc_final: 0.7175 (pt0) REVERT: L 224 LYS cc_start: 0.6017 (ttpp) cc_final: 0.5619 (pttp) REVERT: L 236 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5934 (mt) REVERT: L 283 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.5957 (mpp80) REVERT: L 306 MET cc_start: 0.4615 (mmp) cc_final: 0.4352 (mmp) REVERT: L 321 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6396 (ttt-90) REVERT: L 400 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: M 12 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6273 (mtp180) REVERT: M 17 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.6429 (tmt-80) REVERT: M 75 GLU cc_start: 0.7486 (tp30) cc_final: 0.7069 (tp30) REVERT: M 184 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: M 224 LYS cc_start: 0.6203 (ttpp) cc_final: 0.5780 (pttp) REVERT: M 264 ASN cc_start: 0.5999 (OUTLIER) cc_final: 0.5699 (t0) REVERT: M 400 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6946 (t-90) REVERT: M 403 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6849 (mtt-85) REVERT: M 483 GLU cc_start: 0.7195 (pt0) cc_final: 0.6980 (mt-10) REVERT: N 12 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.6502 (mtp180) REVERT: N 17 ARG cc_start: 0.7276 (ttp-110) cc_final: 0.6489 (tmt-80) REVERT: N 75 GLU cc_start: 0.7453 (tp30) cc_final: 0.6934 (tp30) REVERT: N 79 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7710 (ttpt) REVERT: N 184 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6765 (m-30) REVERT: N 224 LYS cc_start: 0.6060 (ttpp) cc_final: 0.5607 (pttp) REVERT: N 236 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5967 (mt) REVERT: N 306 MET cc_start: 0.4270 (mmp) cc_final: 0.4051 (mmp) REVERT: N 320 LYS cc_start: 0.7180 (tptt) cc_final: 0.6889 (tppt) REVERT: N 400 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.7023 (t-90) REVERT: N 403 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6698 (ttp-170) REVERT: Y 26 HIS cc_start: 0.5350 (OUTLIER) cc_final: 0.5103 (t70) outliers start: 384 outliers final: 182 residues processed: 1131 average time/residue: 1.3186 time to fit residues: 1894.1357 Evaluate side-chains 1121 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 871 time to evaluate : 4.739 ------------------------------------------------------------------------------- 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 184 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 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 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 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 366 GLU 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 15 MET 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 193 GLN 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 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 15 MET Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 79 LYS 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 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 43 PHE 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 168 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 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 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 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 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 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 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 184 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 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 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 15 MET 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 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 15 MET Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 79 LYS 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 L residue 12 ARG Chi-restraints excluded: chain L residue 43 PHE 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 168 VAL 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 321 ARG 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 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 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 88 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 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 Y 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: 4.9990 chunk 645 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 421 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 717 optimal weight: 0.8980 chunk 595 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 376 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 B 36 ASN C 36 ASN C 365 GLN D 365 GLN F 36 ASN F 365 GLN G 36 ASN G 318 GLN G 365 GLN H 36 ASN H 365 GLN I 36 ASN J 36 ASN J 365 GLN K 36 ASN K 365 GLN L 365 GLN M 36 ASN M 365 GLN N 36 ASN N 365 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 56042 Z= 0.191 Angle : 0.538 8.023 75712 Z= 0.281 Chirality : 0.042 0.154 9142 Planarity : 0.003 0.031 9884 Dihedral : 4.616 56.964 7932 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.81 % Favored : 97.00 % Rotamer: Outliers : 5.61 % Allowed : 23.83 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.10), residues: 7462 helix: 2.13 (0.08), residues: 4228 sheet: -0.22 (0.16), residues: 1106 loop : -0.46 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 23 HIS 0.002 0.001 HIS E 400 PHE 0.007 0.001 PHE G 194 TYR 0.012 0.001 TYR D 505 ARG 0.005 0.000 ARG J 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 1220 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 893 time to evaluate : 4.815 Fit side-chains REVERT: A 17 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6422 (tmt-80) REVERT: A 75 GLU cc_start: 0.7460 (tp30) cc_final: 0.7016 (tp30) REVERT: A 79 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7732 (ttpt) REVERT: A 193 GLN cc_start: 0.7335 (pt0) cc_final: 0.7075 (pt0) REVERT: A 213 GLU cc_start: 0.7199 (mp0) cc_final: 0.6717 (mp0) REVERT: A 224 LYS cc_start: 0.6108 (ttpp) cc_final: 0.5718 (pttp) REVERT: A 306 MET cc_start: 0.4262 (mmp) cc_final: 0.3992 (mmp) REVERT: A 400 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6884 (t-90) REVERT: A 403 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6671 (ttp-170) REVERT: A 444 ARG cc_start: 0.7961 (ttm170) cc_final: 0.6835 (tpt90) REVERT: A 483 GLU cc_start: 0.7241 (pt0) cc_final: 0.6990 (mt-10) REVERT: B 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6433 (tmt-80) REVERT: B 75 GLU cc_start: 0.7427 (tp30) cc_final: 0.6993 (tp30) REVERT: B 79 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7529 (mtmm) REVERT: B 224 LYS cc_start: 0.6081 (ttpp) cc_final: 0.5735 (pttp) REVERT: B 400 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: B 403 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6682 (ttp-170) REVERT: C 17 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: C 75 GLU cc_start: 0.7454 (tp30) cc_final: 0.7124 (tp30) REVERT: C 79 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7715 (ttpt) REVERT: C 165 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6800 (mtt) REVERT: C 193 GLN cc_start: 0.7420 (pt0) cc_final: 0.7189 (pt0) REVERT: C 213 GLU cc_start: 0.7033 (mp0) cc_final: 0.6559 (mp0) REVERT: C 224 LYS cc_start: 0.6208 (ttpp) cc_final: 0.5748 (pttp) REVERT: C 236 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5955 (mt) REVERT: C 283 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.5941 (mpp80) REVERT: C 306 MET cc_start: 0.4350 (mmp) cc_final: 0.4059 (mmp) REVERT: C 400 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6954 (t-90) REVERT: D 12 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6302 (mtp180) REVERT: D 17 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6426 (tmt-80) REVERT: D 75 GLU cc_start: 0.7448 (tp30) cc_final: 0.7007 (tp30) REVERT: D 79 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7730 (ttpt) REVERT: D 193 GLN cc_start: 0.7362 (pt0) cc_final: 0.7013 (pt0) REVERT: D 213 GLU cc_start: 0.7103 (mp0) cc_final: 0.6772 (mp0) REVERT: D 224 LYS cc_start: 0.6106 (ttpp) cc_final: 0.5636 (pttp) REVERT: D 306 MET cc_start: 0.4398 (mmp) cc_final: 0.4179 (mmp) REVERT: D 321 ARG cc_start: 0.6788 (ttt90) cc_final: 0.6573 (ttt-90) REVERT: D 400 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6986 (t-90) REVERT: D 403 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6692 (ttp-170) REVERT: E 12 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.6366 (mtp180) REVERT: E 17 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6453 (tmt-80) REVERT: E 75 GLU cc_start: 0.7503 (tp30) cc_final: 0.7005 (tp30) REVERT: E 79 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7705 (ttpt) REVERT: E 193 GLN cc_start: 0.7443 (pt0) cc_final: 0.7155 (pt0) REVERT: E 224 LYS cc_start: 0.6041 (ttpp) cc_final: 0.5684 (pttp) REVERT: E 236 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5898 (mt) REVERT: E 283 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.5904 (mpp80) REVERT: E 306 MET cc_start: 0.4596 (mmp) cc_final: 0.4363 (mmp) REVERT: E 400 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6908 (t-90) REVERT: F 12 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6279 (mtp180) REVERT: F 17 ARG cc_start: 0.7211 (ttp-110) cc_final: 0.6395 (tmt-80) REVERT: F 75 GLU cc_start: 0.7436 (tp30) cc_final: 0.6935 (tp30) REVERT: F 79 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7691 (ttpt) REVERT: F 193 GLN cc_start: 0.7513 (pt0) cc_final: 0.7293 (pt0) REVERT: F 213 GLU cc_start: 0.7148 (mp0) cc_final: 0.6582 (mp0) REVERT: F 224 LYS cc_start: 0.6244 (ttpp) cc_final: 0.5824 (pttp) REVERT: F 264 ASN cc_start: 0.6037 (OUTLIER) cc_final: 0.5723 (t0) REVERT: F 306 MET cc_start: 0.4229 (mmp) cc_final: 0.3998 (mmp) REVERT: F 400 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: F 403 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6684 (ttp-170) REVERT: G 12 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6550 (mtp180) REVERT: G 17 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6460 (tmt-80) REVERT: G 75 GLU cc_start: 0.7474 (tp30) cc_final: 0.6936 (tp30) REVERT: G 79 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7691 (ttpt) REVERT: G 224 LYS cc_start: 0.6144 (ttpp) cc_final: 0.5763 (pttp) REVERT: G 264 ASN cc_start: 0.6174 (OUTLIER) cc_final: 0.5928 (m-40) REVERT: G 306 MET cc_start: 0.4250 (mmp) cc_final: 0.4001 (mmp) REVERT: G 400 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7034 (t-90) REVERT: G 403 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6698 (ttp-170) REVERT: H 17 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6422 (tmt-80) REVERT: H 75 GLU cc_start: 0.7461 (tp30) cc_final: 0.7017 (tp30) REVERT: H 79 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7732 (ttpt) REVERT: H 193 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7079 (pt0) REVERT: H 213 GLU cc_start: 0.7164 (mp0) cc_final: 0.6632 (mp0) REVERT: H 224 LYS cc_start: 0.6103 (ttpp) cc_final: 0.5716 (pttp) REVERT: H 306 MET cc_start: 0.4262 (mmp) cc_final: 0.3992 (mmp) REVERT: H 400 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6883 (t-90) REVERT: H 403 ARG cc_start: 0.7073 (ttm-80) cc_final: 0.6668 (ttp-170) REVERT: H 444 ARG cc_start: 0.7959 (ttm170) cc_final: 0.6839 (tpt90) REVERT: H 483 GLU cc_start: 0.7241 (pt0) cc_final: 0.6992 (mt-10) REVERT: I 12 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6234 (mtp180) REVERT: I 17 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.6430 (tmt-80) REVERT: I 75 GLU cc_start: 0.7426 (tp30) cc_final: 0.6989 (tp30) REVERT: I 79 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7527 (mtmm) REVERT: I 224 LYS cc_start: 0.6090 (ttpp) cc_final: 0.5754 (pttp) REVERT: I 400 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.6908 (t-90) REVERT: I 403 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6681 (ttp-170) REVERT: J 17 ARG cc_start: 0.7269 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: J 75 GLU cc_start: 0.7456 (tp30) cc_final: 0.7126 (tp30) REVERT: J 79 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7728 (ttpt) REVERT: J 165 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6801 (mtt) REVERT: J 193 GLN cc_start: 0.7474 (pt0) cc_final: 0.7224 (pt0) REVERT: J 213 GLU cc_start: 0.7107 (mp0) cc_final: 0.6662 (mp0) REVERT: J 224 LYS cc_start: 0.6198 (ttpp) cc_final: 0.5739 (pttp) REVERT: J 236 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5939 (mt) REVERT: J 283 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5961 (mpp80) REVERT: J 306 MET cc_start: 0.4354 (mmp) cc_final: 0.4043 (mmp) REVERT: J 400 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6930 (t-90) REVERT: K 12 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6304 (mtp180) REVERT: K 17 ARG cc_start: 0.7256 (ttp-110) cc_final: 0.6427 (tmt-80) REVERT: K 75 GLU cc_start: 0.7447 (tp30) cc_final: 0.7006 (tp30) REVERT: K 79 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7732 (ttpt) REVERT: K 193 GLN cc_start: 0.7357 (pt0) cc_final: 0.7019 (pt0) REVERT: K 213 GLU cc_start: 0.7177 (mp0) cc_final: 0.6663 (mp0) REVERT: K 224 LYS cc_start: 0.6108 (ttpp) cc_final: 0.5634 (pttp) REVERT: K 306 MET cc_start: 0.4434 (mmp) cc_final: 0.4215 (mmp) REVERT: K 400 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6993 (t-90) REVERT: K 403 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.6668 (ttp-110) REVERT: L 12 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6363 (mtp180) REVERT: L 17 ARG cc_start: 0.7274 (ttp-110) cc_final: 0.6445 (tmt-80) REVERT: L 75 GLU cc_start: 0.7503 (tp30) cc_final: 0.7051 (tp30) REVERT: L 79 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7708 (ttpt) REVERT: L 190 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7173 (mm-30) REVERT: L 193 GLN cc_start: 0.7444 (pt0) cc_final: 0.7187 (pt0) REVERT: L 213 GLU cc_start: 0.7156 (mp0) cc_final: 0.6640 (mp0) REVERT: L 224 LYS cc_start: 0.5951 (ttpp) cc_final: 0.5579 (pttp) REVERT: L 236 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5936 (mt) REVERT: L 283 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5952 (mpp80) REVERT: L 306 MET cc_start: 0.4598 (mmp) cc_final: 0.4366 (mmp) REVERT: L 400 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6927 (t-90) REVERT: M 12 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6276 (mtp180) REVERT: M 17 ARG cc_start: 0.7207 (ttp-110) cc_final: 0.6390 (tmt-80) REVERT: M 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6935 (tp30) REVERT: M 79 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7700 (ttpt) REVERT: M 193 GLN cc_start: 0.7489 (pt0) cc_final: 0.7257 (pt0) REVERT: M 213 GLU cc_start: 0.7153 (mp0) cc_final: 0.6564 (mp0) REVERT: M 224 LYS cc_start: 0.6219 (ttpp) cc_final: 0.5809 (pttp) REVERT: M 264 ASN cc_start: 0.6024 (OUTLIER) cc_final: 0.5705 (t0) REVERT: M 306 MET cc_start: 0.4215 (mmp) cc_final: 0.3987 (mmp) REVERT: M 400 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.6939 (t-90) REVERT: M 403 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6695 (ttp-170) REVERT: N 12 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6557 (mtp180) REVERT: N 17 ARG cc_start: 0.7247 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: N 75 GLU cc_start: 0.7473 (tp30) cc_final: 0.6935 (tp30) REVERT: N 79 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7693 (ttpt) REVERT: N 224 LYS cc_start: 0.6055 (ttpp) cc_final: 0.5691 (pttp) REVERT: N 236 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.6005 (mt) REVERT: N 306 MET cc_start: 0.4188 (mmp) cc_final: 0.3944 (mmp) REVERT: N 320 LYS cc_start: 0.7216 (tptt) cc_final: 0.6892 (tppt) REVERT: N 321 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.7026 (ttt90) REVERT: N 400 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: N 403 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6707 (ttp-170) REVERT: Y 26 HIS cc_start: 0.5257 (OUTLIER) cc_final: 0.4986 (t70) REVERT: 1 26 HIS cc_start: 0.5433 (OUTLIER) cc_final: 0.5126 (t70) outliers start: 327 outliers final: 162 residues processed: 1123 average time/residue: 1.3167 time to fit residues: 1879.6115 Evaluate side-chains 1097 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 881 time to evaluate : 4.780 ------------------------------------------------------------------------------- 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 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU 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 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 15 MET Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 68 MET 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 186 LEU 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 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 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 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 153 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 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 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 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 193 GLN 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 168 VAL Chi-restraints excluded: chain I residue 176 VAL 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 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 275 VAL Chi-restraints excluded: chain J residue 283 ARG 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 15 MET Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 68 MET 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 168 VAL 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 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 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 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 186 LEU Chi-restraints excluded: chain N residue 236 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 Y 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: 9.9990 chunk 80 optimal weight: 7.9990 chunk 409 optimal weight: 0.8980 chunk 524 optimal weight: 0.0050 chunk 406 optimal weight: 0.9980 chunk 604 optimal weight: 4.9990 chunk 400 optimal weight: 9.9990 chunk 715 optimal weight: 5.9990 chunk 447 optimal weight: 20.0000 chunk 436 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 overall best weight: 2.5798 ------------------------------------------------------------------------------- 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 36 ASN D 365 GLN E 365 GLN F 365 GLN G 318 GLN G 365 GLN H 318 GLN H 365 GLN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 56042 Z= 0.261 Angle : 0.576 10.569 75712 Z= 0.297 Chirality : 0.043 0.159 9142 Planarity : 0.004 0.032 9884 Dihedral : 4.589 50.214 7930 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.71 % Favored : 97.11 % Rotamer: Outliers : 5.58 % Allowed : 23.90 % Favored : 70.52 % 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: 1.49 (0.10), residues: 7462 helix: 2.07 (0.08), residues: 4228 sheet: -0.19 (0.16), residues: 1106 loop : -0.53 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 23 HIS 0.003 0.002 HIS E 400 PHE 0.006 0.001 PHE G 194 TYR 0.015 0.001 TYR K 505 ARG 0.005 0.000 ARG F 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 1217 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 892 time to evaluate : 4.780 Fit side-chains REVERT: A 17 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6407 (tmt-80) REVERT: A 75 GLU cc_start: 0.7469 (tp30) cc_final: 0.7035 (tp30) REVERT: A 79 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7745 (ttpt) REVERT: A 193 GLN cc_start: 0.7369 (pt0) cc_final: 0.7126 (pt0) REVERT: A 213 GLU cc_start: 0.7185 (mp0) cc_final: 0.6676 (mp0) REVERT: A 224 LYS cc_start: 0.6117 (ttpp) cc_final: 0.5740 (pttp) REVERT: A 306 MET cc_start: 0.4315 (mmp) cc_final: 0.4048 (mmp) REVERT: A 400 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.6921 (t-90) REVERT: A 403 ARG cc_start: 0.7093 (ttm-80) cc_final: 0.6640 (ttp-170) REVERT: A 483 GLU cc_start: 0.7261 (pt0) cc_final: 0.7031 (mt-10) REVERT: B 17 ARG cc_start: 0.7265 (ttp-110) cc_final: 0.6459 (tmt-80) REVERT: B 75 GLU cc_start: 0.7472 (tp30) cc_final: 0.7033 (tp30) REVERT: B 79 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7555 (mtmm) REVERT: B 224 LYS cc_start: 0.6164 (ttpp) cc_final: 0.5730 (pttp) REVERT: B 400 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: B 403 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6692 (ttp-170) REVERT: C 17 ARG cc_start: 0.7286 (ttp-110) cc_final: 0.6486 (tmt-80) REVERT: C 75 GLU cc_start: 0.7480 (tp30) cc_final: 0.7164 (tp30) REVERT: C 79 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7735 (ttpt) REVERT: C 165 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6799 (mtt) REVERT: C 224 LYS cc_start: 0.6243 (ttpp) cc_final: 0.5745 (pttp) REVERT: C 236 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5961 (mt) REVERT: C 283 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5903 (mpp80) REVERT: C 306 MET cc_start: 0.4432 (mmp) cc_final: 0.4108 (mmp) REVERT: C 400 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.6915 (t-90) REVERT: D 12 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6289 (mtp180) REVERT: D 17 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6464 (tmt-80) REVERT: D 75 GLU cc_start: 0.7473 (tp30) cc_final: 0.7024 (tp30) REVERT: D 79 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7739 (ttpt) REVERT: D 193 GLN cc_start: 0.7350 (pt0) cc_final: 0.7000 (pt0) REVERT: D 213 GLU cc_start: 0.7116 (mp0) cc_final: 0.6765 (mp0) REVERT: D 224 LYS cc_start: 0.6176 (ttpp) cc_final: 0.5673 (pttp) REVERT: D 306 MET cc_start: 0.4507 (mmp) cc_final: 0.4150 (mmp) REVERT: D 400 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.6993 (t-90) REVERT: D 403 ARG cc_start: 0.7101 (ttm-80) cc_final: 0.6636 (ttp-110) REVERT: E 12 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6379 (mtp180) REVERT: E 17 ARG cc_start: 0.7269 (ttp-110) cc_final: 0.6444 (tmt-80) REVERT: E 75 GLU cc_start: 0.7518 (tp30) cc_final: 0.7056 (tp30) REVERT: E 193 GLN cc_start: 0.7427 (pt0) cc_final: 0.7164 (pt0) REVERT: E 224 LYS cc_start: 0.6109 (ttpp) cc_final: 0.5700 (pttp) REVERT: E 236 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5885 (mt) REVERT: E 283 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.5868 (mpp80) REVERT: E 306 MET cc_start: 0.4541 (mmp) cc_final: 0.4279 (mmp) REVERT: E 400 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.6888 (t-90) REVERT: F 12 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6289 (mtp180) REVERT: F 17 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6407 (tmt-80) REVERT: F 75 GLU cc_start: 0.7446 (tp30) cc_final: 0.6947 (tp30) REVERT: F 79 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: F 224 LYS cc_start: 0.6252 (ttpp) cc_final: 0.5885 (pttp) REVERT: F 264 ASN cc_start: 0.6002 (OUTLIER) cc_final: 0.5688 (t0) REVERT: F 306 MET cc_start: 0.4325 (mmp) cc_final: 0.3988 (mmp) REVERT: F 400 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.6924 (t-90) REVERT: F 403 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6848 (mtt-85) REVERT: G 12 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6573 (mtp180) REVERT: G 17 ARG cc_start: 0.7272 (ttp-110) cc_final: 0.6469 (tmt-80) REVERT: G 75 GLU cc_start: 0.7467 (tp30) cc_final: 0.6960 (tp30) REVERT: G 79 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7700 (ttpt) REVERT: G 224 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5685 (pttp) REVERT: G 264 ASN cc_start: 0.6176 (OUTLIER) cc_final: 0.5605 (t0) REVERT: G 400 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.7009 (t-90) REVERT: G 403 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6670 (ttp-170) REVERT: H 17 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6402 (tmt-80) REVERT: H 75 GLU cc_start: 0.7470 (tp30) cc_final: 0.7036 (tp30) REVERT: H 79 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7743 (ttpt) REVERT: H 193 GLN cc_start: 0.7344 (pt0) cc_final: 0.7098 (pt0) REVERT: H 224 LYS cc_start: 0.6111 (ttpp) cc_final: 0.5737 (pttp) REVERT: H 306 MET cc_start: 0.4314 (mmp) cc_final: 0.4049 (mmp) REVERT: H 321 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6131 (ttt-90) REVERT: H 400 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6920 (t-90) REVERT: H 403 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6641 (ttp-170) REVERT: H 483 GLU cc_start: 0.7263 (pt0) cc_final: 0.7034 (mt-10) REVERT: I 12 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6240 (mtp180) REVERT: I 17 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6456 (tmt-80) REVERT: I 75 GLU cc_start: 0.7472 (tp30) cc_final: 0.7029 (tp30) REVERT: I 79 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7561 (mtmm) REVERT: I 224 LYS cc_start: 0.6161 (ttpp) cc_final: 0.5751 (pttp) REVERT: I 366 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: I 400 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.6905 (t-90) REVERT: I 403 ARG cc_start: 0.7108 (ttm-80) cc_final: 0.6666 (ttp-170) REVERT: J 17 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6487 (tmt-80) REVERT: J 75 GLU cc_start: 0.7463 (tp30) cc_final: 0.7145 (tp30) REVERT: J 79 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7734 (ttpt) REVERT: J 165 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6795 (mtt) REVERT: J 224 LYS cc_start: 0.6232 (ttpp) cc_final: 0.5736 (pttp) REVERT: J 236 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5977 (mt) REVERT: J 283 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.5920 (mpp80) REVERT: J 306 MET cc_start: 0.4424 (mmp) cc_final: 0.4101 (mmp) REVERT: J 400 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.6915 (t-90) REVERT: K 12 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6289 (mtp180) REVERT: K 17 ARG cc_start: 0.7284 (ttp-110) cc_final: 0.6457 (tmt-80) REVERT: K 75 GLU cc_start: 0.7471 (tp30) cc_final: 0.7023 (tp30) REVERT: K 79 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7740 (ttpt) REVERT: K 193 GLN cc_start: 0.7357 (pt0) cc_final: 0.7008 (pt0) REVERT: K 213 GLU cc_start: 0.7185 (mp0) cc_final: 0.6661 (mp0) REVERT: K 224 LYS cc_start: 0.6169 (ttpp) cc_final: 0.5672 (pttp) REVERT: K 306 MET cc_start: 0.4463 (mmp) cc_final: 0.4116 (mmp) REVERT: K 400 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.6999 (t-90) REVERT: K 403 ARG cc_start: 0.7086 (ttm-80) cc_final: 0.6621 (ttp-110) REVERT: L 12 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6379 (mtp180) REVERT: L 17 ARG cc_start: 0.7273 (ttp-110) cc_final: 0.6445 (tmt-80) REVERT: L 75 GLU cc_start: 0.7518 (tp30) cc_final: 0.7052 (tp30) REVERT: L 193 GLN cc_start: 0.7430 (pt0) cc_final: 0.7173 (pt0) REVERT: L 224 LYS cc_start: 0.6035 (ttpp) cc_final: 0.5619 (pttp) REVERT: L 236 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5912 (mt) REVERT: L 283 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5912 (mpp80) REVERT: L 400 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.6897 (t-90) REVERT: M 12 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6289 (mtp180) REVERT: M 17 ARG cc_start: 0.7240 (ttp-110) cc_final: 0.6410 (tmt-80) REVERT: M 75 GLU cc_start: 0.7439 (tp30) cc_final: 0.6945 (tp30) REVERT: M 79 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7725 (ttpt) REVERT: M 213 GLU cc_start: 0.7107 (mp0) cc_final: 0.6571 (mp0) REVERT: M 224 LYS cc_start: 0.6270 (ttpp) cc_final: 0.5967 (pttp) REVERT: M 264 ASN cc_start: 0.6005 (OUTLIER) cc_final: 0.5698 (t0) REVERT: M 306 MET cc_start: 0.4328 (mmp) cc_final: 0.3990 (mmp) REVERT: M 400 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: M 403 ARG cc_start: 0.7106 (ttm-80) cc_final: 0.6666 (ttp-170) REVERT: N 12 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6571 (mtp180) REVERT: N 17 ARG cc_start: 0.7269 (ttp-110) cc_final: 0.6468 (tmt-80) REVERT: N 75 GLU cc_start: 0.7465 (tp30) cc_final: 0.6959 (tp30) REVERT: N 79 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7698 (ttpt) REVERT: N 224 LYS cc_start: 0.6116 (ttpp) cc_final: 0.5688 (pttp) REVERT: N 236 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.6015 (mt) REVERT: N 306 MET cc_start: 0.4278 (mmp) cc_final: 0.3964 (mmp) REVERT: N 320 LYS cc_start: 0.7201 (tptt) cc_final: 0.6869 (tppt) REVERT: N 321 ARG cc_start: 0.7252 (ttm-80) cc_final: 0.7024 (ttt-90) REVERT: N 400 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.7006 (t-90) REVERT: N 403 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6687 (ttp-170) REVERT: Y 26 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.5097 (t70) REVERT: 1 26 HIS cc_start: 0.5452 (OUTLIER) cc_final: 0.5130 (t70) outliers start: 325 outliers final: 176 residues processed: 1119 average time/residue: 1.3418 time to fit residues: 1908.4959 Evaluate side-chains 1107 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 878 time to evaluate : 4.630 ------------------------------------------------------------------------------- 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 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU 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 C residue 15 MET 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 15 MET 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 168 VAL Chi-restraints excluded: chain D residue 186 LEU 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 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 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 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 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 247 LEU Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 275 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 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 88 THR 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 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 321 ARG 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 168 VAL Chi-restraints excluded: chain I residue 176 VAL 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 329 THR Chi-restraints excluded: chain I residue 366 GLU 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 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 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 15 MET 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 168 VAL 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 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 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 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 168 VAL Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 209 THR 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 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 88 THR 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 236 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 Y 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: 9.9990 chunk 427 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 454 optimal weight: 7.9990 chunk 487 optimal weight: 4.9990 chunk 353 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 562 optimal weight: 0.5980 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 E 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 56042 Z= 0.298 Angle : 0.600 10.068 75712 Z= 0.310 Chirality : 0.044 0.164 9142 Planarity : 0.004 0.033 9884 Dihedral : 4.608 59.647 7930 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.01 % Rotamer: Outliers : 5.51 % Allowed : 24.04 % Favored : 70.45 % 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: 1.27 (0.10), residues: 7462 helix: 1.99 (0.08), residues: 4228 sheet: -0.48 (0.17), residues: 966 loop : -0.72 (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 A 400 PHE 0.006 0.001 PHE U 25 TYR 0.017 0.001 TYR D 505 ARG 0.005 0.001 ARG E 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 1209 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 888 time to evaluate : 4.832 Fit side-chains REVERT: A 17 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6421 (tmt-80) REVERT: A 75 GLU cc_start: 0.7476 (tp30) cc_final: 0.7039 (tp30) REVERT: A 79 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7731 (ttpt) REVERT: A 184 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6776 (m-30) REVERT: A 193 GLN cc_start: 0.7320 (pt0) cc_final: 0.7103 (pt0) REVERT: A 224 LYS cc_start: 0.6151 (ttpp) cc_final: 0.5719 (pttp) REVERT: A 306 MET cc_start: 0.4425 (mmp) cc_final: 0.3977 (mmp) REVERT: A 400 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.6903 (t-90) REVERT: A 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6647 (ttp-170) REVERT: B 17 ARG cc_start: 0.7265 (ttp-110) cc_final: 0.6477 (tmt-80) REVERT: B 75 GLU cc_start: 0.7459 (tp30) cc_final: 0.7040 (tp30) REVERT: B 224 LYS cc_start: 0.6144 (ttpp) cc_final: 0.5713 (pttp) REVERT: B 403 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6678 (ttp-170) REVERT: C 17 ARG cc_start: 0.7307 (ttp-110) cc_final: 0.6503 (tmt-80) REVERT: C 75 GLU cc_start: 0.7484 (tp30) cc_final: 0.7041 (tp30) REVERT: C 79 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7731 (ttpt) REVERT: C 165 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6756 (mtt) REVERT: C 184 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6793 (m-30) REVERT: C 224 LYS cc_start: 0.6183 (ttpp) cc_final: 0.5699 (pttp) REVERT: C 236 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5965 (mt) REVERT: C 283 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5870 (mpp80) REVERT: C 306 MET cc_start: 0.4399 (mmp) cc_final: 0.4037 (mmp) REVERT: D 12 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6287 (mtp180) REVERT: D 17 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6456 (tmt-80) REVERT: D 75 GLU cc_start: 0.7490 (tp30) cc_final: 0.7036 (tp30) REVERT: D 79 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7728 (ttpt) REVERT: D 193 GLN cc_start: 0.7328 (pt0) cc_final: 0.6975 (pt0) REVERT: D 213 GLU cc_start: 0.7091 (mp0) cc_final: 0.6591 (mp0) REVERT: D 224 LYS cc_start: 0.6173 (ttpp) cc_final: 0.5664 (pttp) REVERT: D 306 MET cc_start: 0.4234 (mmp) cc_final: 0.3856 (mmp) REVERT: D 400 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.6889 (t-90) REVERT: D 403 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6627 (ttp-110) REVERT: E 12 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6389 (mtp180) REVERT: E 17 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6473 (tmt-80) REVERT: E 75 GLU cc_start: 0.7526 (tp30) cc_final: 0.7070 (tp30) REVERT: E 224 LYS cc_start: 0.6077 (ttpp) cc_final: 0.5614 (pttp) REVERT: E 236 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5949 (mt) REVERT: E 283 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.5825 (mpp80) REVERT: E 306 MET cc_start: 0.4339 (mmp) cc_final: 0.4130 (mmp) REVERT: E 400 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.6846 (t-90) REVERT: F 12 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6289 (mtp180) REVERT: F 17 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6432 (tmt-80) REVERT: F 75 GLU cc_start: 0.7492 (tp30) cc_final: 0.7070 (tp30) REVERT: F 224 LYS cc_start: 0.6200 (ttpp) cc_final: 0.5894 (pttp) REVERT: F 264 ASN cc_start: 0.5966 (OUTLIER) cc_final: 0.5641 (t0) REVERT: F 306 MET cc_start: 0.4341 (mmp) cc_final: 0.3949 (mmp) REVERT: F 400 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6908 (t-90) REVERT: F 403 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6650 (ttp-170) REVERT: G 12 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6525 (mtp180) REVERT: G 17 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.6455 (tmt-80) REVERT: G 75 GLU cc_start: 0.7469 (tp30) cc_final: 0.6959 (tp30) REVERT: G 79 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7691 (ttpt) REVERT: G 224 LYS cc_start: 0.6152 (ttpp) cc_final: 0.5663 (pttp) REVERT: G 264 ASN cc_start: 0.6159 (OUTLIER) cc_final: 0.5614 (t0) REVERT: G 306 MET cc_start: 0.4343 (mmp) cc_final: 0.3895 (mmp) REVERT: G 400 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.7000 (t-90) REVERT: G 403 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6664 (ttp-170) REVERT: H 17 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6423 (tmt-80) REVERT: H 75 GLU cc_start: 0.7478 (tp30) cc_final: 0.7041 (tp30) REVERT: H 79 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7730 (ttpt) REVERT: H 193 GLN cc_start: 0.7316 (pt0) cc_final: 0.7094 (pt0) REVERT: H 224 LYS cc_start: 0.6148 (ttpp) cc_final: 0.5716 (pttp) REVERT: H 306 MET cc_start: 0.4425 (mmp) cc_final: 0.3980 (mmp) REVERT: H 321 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6138 (ttt-90) REVERT: H 400 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6895 (t-90) REVERT: H 403 ARG cc_start: 0.7105 (ttm-80) cc_final: 0.6646 (ttp-170) REVERT: I 12 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6243 (mtp180) REVERT: I 17 ARG cc_start: 0.7258 (ttp-110) cc_final: 0.6466 (tmt-80) REVERT: I 75 GLU cc_start: 0.7461 (tp30) cc_final: 0.7037 (tp30) REVERT: I 224 LYS cc_start: 0.6155 (ttpp) cc_final: 0.5723 (pttp) REVERT: I 366 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: I 400 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.6885 (t-90) REVERT: I 403 ARG cc_start: 0.7102 (ttm-80) cc_final: 0.6785 (mtt-85) REVERT: J 17 ARG cc_start: 0.7306 (ttp-110) cc_final: 0.6503 (tmt-80) REVERT: J 75 GLU cc_start: 0.7486 (tp30) cc_final: 0.7167 (tp30) REVERT: J 79 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7732 (ttpt) REVERT: J 165 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6751 (mtt) REVERT: J 184 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: J 224 LYS cc_start: 0.6190 (ttpp) cc_final: 0.5704 (pttp) REVERT: J 236 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5970 (mt) REVERT: J 283 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.5870 (mpp80) REVERT: J 306 MET cc_start: 0.4384 (mmp) cc_final: 0.4010 (mmp) REVERT: K 12 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6288 (mtp180) REVERT: K 17 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6456 (tmt-80) REVERT: K 75 GLU cc_start: 0.7488 (tp30) cc_final: 0.7035 (tp30) REVERT: K 79 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7726 (ttpt) REVERT: K 193 GLN cc_start: 0.7330 (pt0) cc_final: 0.7002 (pt0) REVERT: K 213 GLU cc_start: 0.7184 (mp0) cc_final: 0.6666 (mp0) REVERT: K 224 LYS cc_start: 0.6155 (ttpp) cc_final: 0.5638 (pttp) REVERT: K 306 MET cc_start: 0.4279 (mmp) cc_final: 0.3903 (mmp) REVERT: K 400 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.6940 (t-90) REVERT: K 403 ARG cc_start: 0.7073 (ttm-80) cc_final: 0.6612 (ttp-110) REVERT: L 12 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6384 (mtp180) REVERT: L 17 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6465 (tmt-80) REVERT: L 75 GLU cc_start: 0.7524 (tp30) cc_final: 0.7068 (tp30) REVERT: L 224 LYS cc_start: 0.6032 (ttpp) cc_final: 0.5631 (pttp) REVERT: L 283 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5881 (mpp80) REVERT: L 400 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6865 (t-90) REVERT: M 12 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6275 (mtp180) REVERT: M 17 ARG cc_start: 0.7257 (ttp-110) cc_final: 0.6430 (tmt-80) REVERT: M 75 GLU cc_start: 0.7492 (tp30) cc_final: 0.7069 (tp30) REVERT: M 213 GLU cc_start: 0.7127 (mp0) cc_final: 0.6585 (mp0) REVERT: M 224 LYS cc_start: 0.6215 (ttpp) cc_final: 0.5771 (pttp) REVERT: M 264 ASN cc_start: 0.5961 (OUTLIER) cc_final: 0.5644 (t0) REVERT: M 306 MET cc_start: 0.4354 (mmp) cc_final: 0.3955 (mmp) REVERT: M 400 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.6931 (t-90) REVERT: M 403 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6649 (ttp-170) REVERT: N 12 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6492 (mtp180) REVERT: N 17 ARG cc_start: 0.7254 (ttp-110) cc_final: 0.6452 (tmt-80) REVERT: N 75 GLU cc_start: 0.7467 (tp30) cc_final: 0.6954 (tp30) REVERT: N 79 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7690 (ttpt) REVERT: N 184 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6894 (m-30) REVERT: N 224 LYS cc_start: 0.6098 (ttpp) cc_final: 0.5594 (pttp) REVERT: N 236 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.6042 (mt) REVERT: N 306 MET cc_start: 0.4244 (mmp) cc_final: 0.4024 (mmp) REVERT: N 321 ARG cc_start: 0.7285 (ttm-80) cc_final: 0.7067 (ttt-90) REVERT: N 400 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6971 (t-90) REVERT: N 403 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6675 (ttp-170) REVERT: Y 26 HIS cc_start: 0.5496 (OUTLIER) cc_final: 0.5189 (t70) REVERT: 1 26 HIS cc_start: 0.5461 (OUTLIER) cc_final: 0.5147 (t70) outliers start: 321 outliers final: 191 residues processed: 1106 average time/residue: 1.3536 time to fit residues: 1897.0995 Evaluate side-chains 1119 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 879 time to evaluate : 4.684 ------------------------------------------------------------------------------- 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 184 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 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 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 15 MET 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 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 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 15 MET Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 79 LYS 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 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 366 GLU 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 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 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 331 ILE 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 264 ASN Chi-restraints excluded: chain F residue 275 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 F residue 419 ILE Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 47 THR 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 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 276 LYS 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 321 ARG 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 168 VAL Chi-restraints excluded: chain I residue 176 VAL 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 366 GLU 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 15 MET 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 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 283 ARG 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 15 MET Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 79 LYS 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 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 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 168 VAL Chi-restraints excluded: chain L residue 186 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 331 ILE 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 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 186 LEU Chi-restraints excluded: chain M residue 209 THR 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 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 47 THR 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 168 VAL Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 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 N residue 419 ILE Chi-restraints excluded: chain Y 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: 5.9990 chunk 685 optimal weight: 1.9990 chunk 625 optimal weight: 0.7980 chunk 666 optimal weight: 0.6980 chunk 684 optimal weight: 2.9990 chunk 401 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 523 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 602 optimal weight: 0.0970 chunk 630 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 365 GLN C 365 GLN D 365 GLN E 36 ASN E 365 GLN F 365 GLN G 365 GLN H 318 GLN H 365 GLN I 365 GLN J 365 GLN K 365 GLN L 36 ASN L 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 56042 Z= 0.154 Angle : 0.531 9.241 75712 Z= 0.277 Chirality : 0.041 0.168 9142 Planarity : 0.003 0.032 9884 Dihedral : 4.332 57.522 7929 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.65 % Favored : 97.16 % Rotamer: Outliers : 4.48 % Allowed : 24.91 % Favored : 70.60 % 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: 1.69 (0.10), residues: 7462 helix: 2.23 (0.08), residues: 4242 sheet: -0.10 (0.16), residues: 1106 loop : -0.46 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP T 18 HIS 0.002 0.001 HIS B 400 PHE 0.007 0.001 PHE G 194 TYR 0.010 0.001 TYR K 505 ARG 0.005 0.000 ARG F 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 1151 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 890 time to evaluate : 4.905 Fit side-chains REVERT: A 17 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6392 (tmt-80) REVERT: A 75 GLU cc_start: 0.7462 (tp30) cc_final: 0.7144 (tp30) REVERT: A 79 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: A 193 GLN cc_start: 0.7354 (pt0) cc_final: 0.7112 (pt0) REVERT: A 224 LYS cc_start: 0.6169 (ttpp) cc_final: 0.5736 (pttp) REVERT: A 306 MET cc_start: 0.4477 (mmp) cc_final: 0.4191 (mmp) REVERT: A 400 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.6869 (t-90) REVERT: A 403 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6664 (ttp-170) REVERT: A 444 ARG cc_start: 0.7993 (ttm170) cc_final: 0.6843 (tpt90) REVERT: B 17 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.6438 (tmt-80) REVERT: B 75 GLU cc_start: 0.7397 (tp30) cc_final: 0.6943 (tp30) REVERT: B 79 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7635 (ttpt) REVERT: B 224 LYS cc_start: 0.6215 (ttpp) cc_final: 0.5778 (pttp) REVERT: B 403 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6704 (ttp-170) REVERT: C 17 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.6450 (tmt-80) REVERT: C 75 GLU cc_start: 0.7444 (tp30) cc_final: 0.7184 (tp30) REVERT: C 79 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7757 (ttpt) REVERT: C 165 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6720 (mtt) REVERT: C 193 GLN cc_start: 0.7520 (pt0) cc_final: 0.7221 (pt0) REVERT: C 224 LYS cc_start: 0.6255 (ttpp) cc_final: 0.5790 (pttp) REVERT: C 283 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5888 (mpp80) REVERT: C 400 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6875 (t-90) REVERT: D 12 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6259 (mtp180) REVERT: D 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6406 (tmt-80) REVERT: D 75 GLU cc_start: 0.7430 (tp30) cc_final: 0.6977 (tp30) REVERT: D 79 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7746 (ttpt) REVERT: D 193 GLN cc_start: 0.7338 (pt0) cc_final: 0.7029 (pt0) REVERT: D 213 GLU cc_start: 0.7150 (mp0) cc_final: 0.6577 (mp0) REVERT: D 224 LYS cc_start: 0.6193 (ttpp) cc_final: 0.5822 (pttp) REVERT: D 400 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6945 (t-90) REVERT: D 403 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.6659 (ttp-110) REVERT: E 12 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6331 (mtp180) REVERT: E 17 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6442 (tmt-80) REVERT: E 75 GLU cc_start: 0.7495 (tp30) cc_final: 0.7062 (tp30) REVERT: E 79 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7717 (ttpt) REVERT: E 224 LYS cc_start: 0.6067 (ttpp) cc_final: 0.5666 (pttp) REVERT: E 236 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5946 (mt) REVERT: E 283 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.5959 (mpp80) REVERT: E 400 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: F 17 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6388 (tmt-80) REVERT: F 75 GLU cc_start: 0.7404 (tp30) cc_final: 0.6958 (tp30) REVERT: F 79 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7723 (ttpt) REVERT: F 193 GLN cc_start: 0.7534 (pt0) cc_final: 0.7330 (pt0) REVERT: F 224 LYS cc_start: 0.6211 (ttpp) cc_final: 0.5914 (pttp) REVERT: F 264 ASN cc_start: 0.5960 (OUTLIER) cc_final: 0.5655 (t0) REVERT: F 306 MET cc_start: 0.4338 (mmp) cc_final: 0.4087 (mmp) REVERT: F 400 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.6942 (t-90) REVERT: F 403 ARG cc_start: 0.7121 (ttm-80) cc_final: 0.6694 (ttp-170) REVERT: F 444 ARG cc_start: 0.7945 (ttp80) cc_final: 0.6762 (tpt90) REVERT: G 12 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6530 (mtp180) REVERT: G 17 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6454 (tmt-80) REVERT: G 75 GLU cc_start: 0.7460 (tp30) cc_final: 0.6937 (tp30) REVERT: G 79 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7697 (ttpt) REVERT: G 224 LYS cc_start: 0.6180 (ttpp) cc_final: 0.5715 (pttp) REVERT: G 264 ASN cc_start: 0.6131 (OUTLIER) cc_final: 0.5888 (m-40) REVERT: G 306 MET cc_start: 0.4295 (mmp) cc_final: 0.3827 (mmp) REVERT: G 321 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.7013 (ttt-90) REVERT: G 388 MET cc_start: 0.6041 (tpt) cc_final: 0.5709 (tpp) REVERT: G 400 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.7042 (t-90) REVERT: G 403 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6706 (ttp-170) REVERT: H 17 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6393 (tmt-80) REVERT: H 75 GLU cc_start: 0.7462 (tp30) cc_final: 0.7142 (tp30) REVERT: H 79 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7727 (ttpt) REVERT: H 224 LYS cc_start: 0.6168 (ttpp) cc_final: 0.5734 (pttp) REVERT: H 306 MET cc_start: 0.4470 (mmp) cc_final: 0.4186 (mmp) REVERT: H 400 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6865 (t-90) REVERT: H 403 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6685 (ttp-170) REVERT: H 444 ARG cc_start: 0.8006 (ttm170) cc_final: 0.6852 (tpt90) REVERT: I 12 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6320 (mtp180) REVERT: I 17 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6438 (tmt-80) REVERT: I 75 GLU cc_start: 0.7391 (tp30) cc_final: 0.6963 (tp30) REVERT: I 224 LYS cc_start: 0.6212 (ttpp) cc_final: 0.5785 (pttp) REVERT: I 403 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6720 (ttp-170) REVERT: J 17 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.6450 (tmt-80) REVERT: J 75 GLU cc_start: 0.7440 (tp30) cc_final: 0.7184 (tp30) REVERT: J 79 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7756 (ttpt) REVERT: J 165 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6720 (mtt) REVERT: J 193 GLN cc_start: 0.7529 (pt0) cc_final: 0.7242 (pt0) REVERT: J 224 LYS cc_start: 0.6278 (ttpp) cc_final: 0.5819 (pttp) REVERT: J 283 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.5884 (mpp80) REVERT: J 400 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.6870 (t-90) REVERT: K 12 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6254 (mtp180) REVERT: K 17 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6398 (tmt-80) REVERT: K 75 GLU cc_start: 0.7428 (tp30) cc_final: 0.6978 (tp30) REVERT: K 79 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7745 (ttpt) REVERT: K 193 GLN cc_start: 0.7356 (pt0) cc_final: 0.7034 (pt0) REVERT: K 213 GLU cc_start: 0.7252 (mp0) cc_final: 0.6717 (mp0) REVERT: K 224 LYS cc_start: 0.6182 (ttpp) cc_final: 0.5811 (pttp) REVERT: K 399 LEU cc_start: 0.7357 (tp) cc_final: 0.7057 (tt) REVERT: K 400 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: K 403 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6595 (ttp-110) REVERT: L 12 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6329 (mtp180) REVERT: L 17 ARG cc_start: 0.7258 (ttp-110) cc_final: 0.6440 (tmt-80) REVERT: L 75 GLU cc_start: 0.7495 (tp30) cc_final: 0.7063 (tp30) REVERT: L 79 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7702 (ttpt) REVERT: L 224 LYS cc_start: 0.6076 (ttpp) cc_final: 0.5614 (pttp) REVERT: L 283 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.5937 (mpp80) REVERT: L 400 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.6913 (t-90) REVERT: M 12 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6234 (mtp180) REVERT: M 17 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6391 (tmt-80) REVERT: M 75 GLU cc_start: 0.7405 (tp30) cc_final: 0.6962 (tp30) REVERT: M 79 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7728 (ttpt) REVERT: M 193 GLN cc_start: 0.7553 (pt0) cc_final: 0.7347 (pt0) REVERT: M 224 LYS cc_start: 0.6324 (ttpp) cc_final: 0.5990 (pttp) REVERT: M 264 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5648 (t0) REVERT: M 306 MET cc_start: 0.4362 (mmp) cc_final: 0.4077 (mmp) REVERT: M 400 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6944 (t-90) REVERT: M 403 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6732 (ttp-170) REVERT: M 444 ARG cc_start: 0.7952 (ttm110) cc_final: 0.6735 (tpt90) REVERT: N 12 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6540 (mtp180) REVERT: N 17 ARG cc_start: 0.7241 (ttp-110) cc_final: 0.6451 (tmt-80) REVERT: N 75 GLU cc_start: 0.7451 (tp30) cc_final: 0.6927 (tp30) REVERT: N 79 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7696 (ttpt) REVERT: N 224 LYS cc_start: 0.6124 (ttpp) cc_final: 0.5663 (pttp) REVERT: N 236 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.6002 (mt) REVERT: N 400 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7023 (t-90) REVERT: N 403 ARG cc_start: 0.7129 (ttm-80) cc_final: 0.6706 (ttp-170) REVERT: Y 26 HIS cc_start: 0.5352 (OUTLIER) cc_final: 0.5037 (t70) REVERT: 1 26 HIS cc_start: 0.5376 (OUTLIER) cc_final: 0.5066 (t70) outliers start: 261 outliers final: 145 residues processed: 1079 average time/residue: 1.2993 time to fit residues: 1784.2672 Evaluate side-chains 1067 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 876 time to evaluate : 4.713 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 60 GLU Chi-restraints excluded: chain D residue 79 LYS 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 60 GLU Chi-restraints excluded: chain E residue 79 LYS 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 283 ARG 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 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 264 ASN Chi-restraints excluded: chain F residue 275 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 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 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 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 168 VAL 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 329 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL 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 168 VAL Chi-restraints excluded: chain J residue 186 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 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 79 LYS 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 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 168 VAL Chi-restraints excluded: chain L residue 186 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 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 186 LEU Chi-restraints excluded: chain M residue 209 THR 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 232 MET Chi-restraints excluded: chain N residue 236 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 Chi-restraints excluded: chain N residue 419 ILE 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: 1.9990 chunk 437 optimal weight: 0.0010 chunk 704 optimal weight: 6.9990 chunk 430 optimal weight: 6.9990 chunk 334 optimal weight: 7.9990 chunk 489 optimal weight: 4.9990 chunk 739 optimal weight: 20.0000 chunk 680 optimal weight: 0.0270 chunk 588 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 454 optimal weight: 0.9990 overall best weight: 1.0050 ------------------------------------------------------------------------------- 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 H 365 GLN J 365 GLN K 365 GLN M 365 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3135 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= 0.163 Angle : 0.547 10.614 75712 Z= 0.284 Chirality : 0.041 0.174 9142 Planarity : 0.003 0.033 9884 Dihedral : 4.234 56.685 7923 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.75 % Favored : 97.07 % Rotamer: Outliers : 4.04 % Allowed : 25.62 % 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: 1.73 (0.10), residues: 7462 helix: 2.28 (0.08), residues: 4242 sheet: -0.09 (0.16), residues: 1106 loop : -0.46 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 23 HIS 0.002 0.001 HIS J 400 PHE 0.005 0.001 PHE B 194 TYR 0.011 0.001 TYR K 505 ARG 0.005 0.000 ARG F 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 1116 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 881 time to evaluate : 4.762 Fit side-chains REVERT: A 17 ARG cc_start: 0.7238 (ttp-110) cc_final: 0.6413 (tmt-80) REVERT: A 75 GLU cc_start: 0.7450 (tp30) cc_final: 0.7187 (tp30) REVERT: A 79 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7767 (ttpt) REVERT: A 224 LYS cc_start: 0.6211 (ttpp) cc_final: 0.5754 (pttp) REVERT: A 400 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6898 (t-90) REVERT: A 403 ARG cc_start: 0.7063 (ttm-80) cc_final: 0.6596 (ttp-110) REVERT: A 444 ARG cc_start: 0.8001 (ttm170) cc_final: 0.6844 (tpt90) REVERT: B 17 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6425 (tmt-80) REVERT: B 75 GLU cc_start: 0.7407 (tp30) cc_final: 0.6955 (tp30) REVERT: B 79 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7672 (ttpt) REVERT: B 224 LYS cc_start: 0.6232 (ttpp) cc_final: 0.5860 (pttp) REVERT: B 403 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6697 (ttp-170) REVERT: C 17 ARG cc_start: 0.7279 (ttp-110) cc_final: 0.6462 (tmt-80) REVERT: C 75 GLU cc_start: 0.7441 (tp30) cc_final: 0.7181 (tp30) REVERT: C 79 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7784 (ttpt) REVERT: C 165 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6708 (mtt) REVERT: C 193 GLN cc_start: 0.7527 (pt0) cc_final: 0.7231 (pt0) REVERT: C 224 LYS cc_start: 0.6261 (ttpp) cc_final: 0.5740 (pttp) REVERT: C 283 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.5875 (mpp80) REVERT: C 400 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: D 12 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6279 (mtp180) REVERT: D 17 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.6441 (tmt-80) REVERT: D 75 GLU cc_start: 0.7437 (tp30) cc_final: 0.6984 (tp30) REVERT: D 79 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7764 (ttpt) REVERT: D 193 GLN cc_start: 0.7404 (pt0) cc_final: 0.7073 (pt0) REVERT: D 213 GLU cc_start: 0.7140 (mp0) cc_final: 0.6596 (mp0) REVERT: D 224 LYS cc_start: 0.6227 (ttpp) cc_final: 0.5811 (pttp) REVERT: D 300 ILE cc_start: 0.6372 (pt) cc_final: 0.6150 (pt) REVERT: D 403 ARG cc_start: 0.7086 (ttm-80) cc_final: 0.6642 (ttp-110) REVERT: E 12 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6329 (mtp180) REVERT: E 17 ARG cc_start: 0.7286 (ttp-110) cc_final: 0.6461 (tmt-80) REVERT: E 75 GLU cc_start: 0.7477 (tp30) cc_final: 0.7064 (tp30) REVERT: E 79 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7793 (ttpt) REVERT: E 224 LYS cc_start: 0.6097 (ttpp) cc_final: 0.5719 (pttp) REVERT: E 236 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5958 (mt) REVERT: E 283 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5948 (mpp80) REVERT: E 400 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6905 (t-90) REVERT: F 12 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6238 (mtp180) REVERT: F 17 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.6401 (tmt-80) REVERT: F 75 GLU cc_start: 0.7420 (tp30) cc_final: 0.6958 (tp30) REVERT: F 79 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7770 (ttpt) REVERT: F 224 LYS cc_start: 0.6230 (ttpp) cc_final: 0.5939 (pttp) REVERT: F 264 ASN cc_start: 0.5910 (OUTLIER) cc_final: 0.5609 (t0) REVERT: F 306 MET cc_start: 0.4328 (mmp) cc_final: 0.4078 (mmp) REVERT: F 400 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6948 (t-90) REVERT: F 403 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6687 (ttp-170) REVERT: F 444 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6769 (tpt90) REVERT: G 12 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.6545 (mtp180) REVERT: G 17 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6456 (tmt-80) REVERT: G 75 GLU cc_start: 0.7467 (tp30) cc_final: 0.6946 (tp30) REVERT: G 79 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7730 (ttpt) REVERT: G 224 LYS cc_start: 0.6154 (ttpp) cc_final: 0.5733 (pttp) REVERT: G 306 MET cc_start: 0.4317 (mmp) cc_final: 0.3874 (mmp) REVERT: G 321 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.7034 (ttt-90) REVERT: G 388 MET cc_start: 0.6027 (tpt) cc_final: 0.5712 (tpp) REVERT: G 400 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.7072 (t-90) REVERT: G 403 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6700 (ttp-170) REVERT: H 17 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6413 (tmt-80) REVERT: H 75 GLU cc_start: 0.7450 (tp30) cc_final: 0.7187 (tp30) REVERT: H 79 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7764 (ttpt) REVERT: H 224 LYS cc_start: 0.6211 (ttpp) cc_final: 0.5753 (pttp) REVERT: H 403 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.6614 (ttp-110) REVERT: H 444 ARG cc_start: 0.8002 (ttm170) cc_final: 0.6844 (tpt90) REVERT: I 12 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6326 (mtp180) REVERT: I 17 ARG cc_start: 0.7249 (ttp-110) cc_final: 0.6439 (tmt-80) REVERT: I 75 GLU cc_start: 0.7405 (tp30) cc_final: 0.6952 (tp30) REVERT: I 79 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7670 (ttpt) REVERT: I 224 LYS cc_start: 0.6181 (ttpp) cc_final: 0.5812 (pttp) REVERT: I 403 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6707 (ttp-170) REVERT: J 17 ARG cc_start: 0.7281 (ttp-110) cc_final: 0.6460 (tmt-80) REVERT: J 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.7180 (tp30) REVERT: J 79 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7782 (ttpt) REVERT: J 165 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6693 (mtt) REVERT: J 193 GLN cc_start: 0.7540 (pt0) cc_final: 0.7254 (pt0) REVERT: J 224 LYS cc_start: 0.6266 (ttpp) cc_final: 0.5750 (pttp) REVERT: J 283 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.5869 (mpp80) REVERT: J 400 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.6951 (t-90) REVERT: K 12 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6279 (mtp180) REVERT: K 17 ARG cc_start: 0.7247 (ttp-110) cc_final: 0.6430 (tmt-80) REVERT: K 75 GLU cc_start: 0.7438 (tp30) cc_final: 0.6988 (tp30) REVERT: K 79 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7761 (ttpt) REVERT: K 193 GLN cc_start: 0.7428 (pt0) cc_final: 0.7104 (pt0) REVERT: K 224 LYS cc_start: 0.6207 (ttpp) cc_final: 0.5750 (pttp) REVERT: K 300 ILE cc_start: 0.6375 (pt) cc_final: 0.6159 (pt) REVERT: K 400 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7001 (t-90) REVERT: K 403 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6651 (ttp-110) REVERT: L 12 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6333 (mtp180) REVERT: L 17 ARG cc_start: 0.7273 (ttp-110) cc_final: 0.6455 (tmt-80) REVERT: L 75 GLU cc_start: 0.7468 (tp30) cc_final: 0.7057 (tp30) REVERT: L 79 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7793 (ttpt) REVERT: L 224 LYS cc_start: 0.6132 (ttpp) cc_final: 0.5679 (pttp) REVERT: L 283 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5950 (mpp80) REVERT: M 12 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6260 (mtp180) REVERT: M 17 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6403 (tmt-80) REVERT: M 75 GLU cc_start: 0.7420 (tp30) cc_final: 0.6958 (tp30) REVERT: M 79 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7776 (ttpt) REVERT: M 224 LYS cc_start: 0.6360 (ttpp) cc_final: 0.5979 (pttp) REVERT: M 264 ASN cc_start: 0.5919 (OUTLIER) cc_final: 0.5613 (t0) REVERT: M 306 MET cc_start: 0.4306 (mmp) cc_final: 0.4056 (mmp) REVERT: M 388 MET cc_start: 0.5957 (tpt) cc_final: 0.5662 (tpp) REVERT: M 400 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6965 (t-90) REVERT: M 403 ARG cc_start: 0.7104 (ttm-80) cc_final: 0.6681 (ttp-170) REVERT: M 444 ARG cc_start: 0.7959 (ttm110) cc_final: 0.6748 (tpt90) REVERT: N 12 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.6522 (mtp180) REVERT: N 17 ARG cc_start: 0.7247 (ttp-110) cc_final: 0.6455 (tmt-80) REVERT: N 75 GLU cc_start: 0.7464 (tp30) cc_final: 0.6942 (tp30) REVERT: N 79 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7726 (ttpt) REVERT: N 224 LYS cc_start: 0.6188 (ttpp) cc_final: 0.5747 (pttp) REVERT: N 236 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.6005 (mt) REVERT: N 400 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7054 (t-90) REVERT: N 403 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6698 (ttp-170) REVERT: Y 26 HIS cc_start: 0.5221 (OUTLIER) cc_final: 0.4960 (t70) REVERT: 1 26 HIS cc_start: 0.5335 (OUTLIER) cc_final: 0.5029 (t70) outliers start: 235 outliers final: 149 residues processed: 1051 average time/residue: 1.3180 time to fit residues: 1758.1034 Evaluate side-chains 1064 residues out of total 5824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 870 time to evaluate : 4.782 ------------------------------------------------------------------------------- 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 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 186 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 247 LEU 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 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 275 VAL Chi-restraints excluded: chain C residue 283 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 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 168 VAL Chi-restraints excluded: chain D residue 176 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 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 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 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 264 ASN Chi-restraints excluded: chain F residue 275 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 F residue 444 ARG 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 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 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 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 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 168 VAL Chi-restraints excluded: chain J residue 186 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 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 79 LYS 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 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 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 168 VAL Chi-restraints excluded: chain L residue 186 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 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 186 LEU Chi-restraints excluded: chain M residue 209 THR 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 331 ILE 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 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 236 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 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: 8.9990 chunk 467 optimal weight: 2.9990 chunk 627 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 542 optimal weight: 0.0770 chunk 86 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 589 optimal weight: 5.9990 chunk 246 optimal weight: 0.3980 chunk 605 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 overall best weight: 3.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN B 365 GLN C 365 GLN D 365 GLN E 365 GLN F 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 = 0.4321 r_free = 0.4321 target = 0.205854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124924 restraints weight = 54851.271| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.69 r_work: 0.3262 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 56042 Z= 0.298 Angle : 0.603 10.091 75712 Z= 0.313 Chirality : 0.044 0.183 9142 Planarity : 0.004 0.033 9884 Dihedral : 4.389 51.501 7923 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.79 % Favored : 97.02 % Rotamer: Outliers : 4.26 % Allowed : 25.72 % Favored : 70.02 % 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: 1.36 (0.10), residues: 7462 helix: 2.08 (0.08), residues: 4242 sheet: -1.06 (0.18), residues: 826 loop : -0.48 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 23 HIS 0.004 0.002 HIS A 400 PHE 0.011 0.001 PHE U 25 TYR 0.015 0.001 TYR K 505 ARG 0.005 0.001 ARG E 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27673.24 seconds wall clock time: 475 minutes 17.60 seconds (28517.60 seconds total)