Starting phenix.real_space_refine on Fri Jan 17 07:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s32_19687/01_2025/8s32_19687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s32_19687/01_2025/8s32_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/cci-nas-00/data/ceres_data/8s32_19687/01_2025/8s32_19687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s32_19687/01_2025/8s32_19687.map" model { file = "/net/cci-nas-00/data/ceres_data/8s32_19687/01_2025/8s32_19687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s32_19687/01_2025/8s32_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 10.83, per 1000 atoms: 0.19 Number of scatterers: 55552 At special positions: 0 Unit cell: (155.767, 155.767, 159.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 294 16.00 O 11060 8.00 N 9562 7.00 C 34636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.59 Conformation dependent library (CDL) restraints added in 5.8 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: 5.80 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: 28.36 Time building geometry restraints manager: 12.60 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: 0.39 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain 'O' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' 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: 7.290 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: 0.070 Extract box with map and model: 1.770 Check model and map are aligned: 0.310 Set scattering table: 0.400 Process input model: 93.020 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.480 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: 0.030 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.630 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 94 poor density : 1394 time to evaluate : 4.537 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: 1.5337 time to fit residues: 2736.3939 Evaluate side-chains 948 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 917 time to evaluate : 4.567 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.207621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129350 restraints weight = 55417.469| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.09 r_work: 0.3244 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 to be fit. rotamer outliers: 308 poor density : 959 time to evaluate : 4.557 Fit side-chains REVERT: A 17 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7245 (tmt-80) REVERT: A 75 GLU cc_start: 0.8266 (tp30) cc_final: 0.7772 (tp30) REVERT: A 79 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7987 (ttpt) REVERT: A 184 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.6410 (m-30) REVERT: A 192 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7134 (ppp) REVERT: A 213 GLU cc_start: 0.7200 (mp0) cc_final: 0.6862 (mp0) REVERT: A 224 LYS cc_start: 0.6180 (ttpp) cc_final: 0.5882 (pttp) REVERT: A 397 ASP cc_start: 0.7027 (m-30) cc_final: 0.6755 (t0) REVERT: A 403 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7203 (ttp-170) REVERT: A 444 ARG cc_start: 0.8536 (ttp80) cc_final: 0.7402 (tpt90) REVERT: A 483 GLU cc_start: 0.8058 (pt0) cc_final: 0.7508 (mt-10) REVERT: B 17 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7154 (tmt-80) REVERT: B 58 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8034 (mm-30) REVERT: B 75 GLU cc_start: 0.8270 (tp30) cc_final: 0.7777 (tp30) REVERT: B 79 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8021 (ttpt) REVERT: B 110 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.7461 (mtm) REVERT: B 184 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6426 (m-30) REVERT: B 192 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7135 (ppp) REVERT: B 213 GLU cc_start: 0.7230 (mp0) cc_final: 0.6829 (mp0) REVERT: B 224 LYS cc_start: 0.6252 (ttpp) cc_final: 0.5780 (pttp) REVERT: B 397 ASP cc_start: 0.7022 (m-30) cc_final: 0.6722 (t0) REVERT: B 403 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7204 (ttp-170) REVERT: C 17 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7257 (tmt-80) REVERT: C 75 GLU cc_start: 0.8258 (tp30) cc_final: 0.7913 (tp30) REVERT: C 79 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7950 (ttpt) REVERT: C 165 MET cc_start: 0.7546 (mtm) cc_final: 0.7199 (mtt) REVERT: C 184 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6395 (m-30) REVERT: C 192 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7160 (ppp) REVERT: C 193 GLN cc_start: 0.7778 (pt0) cc_final: 0.7512 (pt0) REVERT: C 213 GLU cc_start: 0.7187 (mp0) cc_final: 0.6790 (mp0) REVERT: C 224 LYS cc_start: 0.6256 (ttpp) cc_final: 0.5798 (pttp) REVERT: C 397 ASP cc_start: 0.7110 (m-30) cc_final: 0.6825 (t0) REVERT: D 12 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.6854 (mtp180) REVERT: D 17 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7169 (tmt-80) REVERT: D 75 GLU cc_start: 0.8279 (tp30) cc_final: 0.7804 (tp30) REVERT: D 165 MET cc_start: 0.7507 (mtm) cc_final: 0.7292 (mtt) REVERT: D 184 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6390 (m-30) REVERT: D 192 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7188 (ppp) REVERT: D 224 LYS cc_start: 0.6243 (ttpp) cc_final: 0.5751 (pttp) REVERT: D 397 ASP cc_start: 0.7029 (m-30) cc_final: 0.6775 (t0) REVERT: D 403 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7221 (ttp-170) REVERT: E 12 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.6957 (mtp180) REVERT: E 17 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.7283 (tmt-80) REVERT: E 75 GLU cc_start: 0.8321 (tp30) cc_final: 0.7771 (tp30) REVERT: E 79 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7967 (ttpt) REVERT: E 184 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6492 (m-30) REVERT: E 190 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7345 (mm-30) REVERT: E 192 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7063 (ppp) REVERT: E 193 GLN cc_start: 0.7654 (pt0) cc_final: 0.7406 (pt0) REVERT: E 224 LYS cc_start: 0.6157 (ttpp) cc_final: 0.5782 (pttp) REVERT: E 397 ASP cc_start: 0.7031 (m-30) cc_final: 0.6735 (t0) REVERT: F 12 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.6859 (mtp180) REVERT: F 17 ARG cc_start: 0.8227 (ttp-110) cc_final: 0.7211 (tmt-80) REVERT: F 75 GLU cc_start: 0.8344 (tp30) cc_final: 0.7831 (tp30) REVERT: F 79 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: F 193 GLN cc_start: 0.7674 (pt0) cc_final: 0.7413 (pt0) REVERT: F 213 GLU cc_start: 0.7267 (mp0) cc_final: 0.6836 (mp0) REVERT: F 224 LYS cc_start: 0.6266 (ttpp) cc_final: 0.5926 (pttp) REVERT: F 225 LYS cc_start: 0.7261 (mtmm) cc_final: 0.6622 (mtpp) REVERT: F 397 ASP cc_start: 0.7049 (m-30) cc_final: 0.6778 (t0) REVERT: F 400 HIS cc_start: 0.7515 (m-70) cc_final: 0.7169 (t-90) REVERT: F 403 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7161 (ttp-170) REVERT: F 444 ARG cc_start: 0.8569 (ttp80) cc_final: 0.7370 (tpt90) REVERT: G 12 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7183 (mtp180) REVERT: G 17 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7259 (tmt-80) REVERT: G 75 GLU cc_start: 0.8317 (tp30) cc_final: 0.7761 (tp30) REVERT: G 165 MET cc_start: 0.7576 (mtm) cc_final: 0.7244 (mtt) REVERT: G 184 ASP cc_start: 0.6723 (OUTLIER) cc_final: 0.6418 (m-30) REVERT: G 193 GLN cc_start: 0.7800 (pt0) cc_final: 0.7537 (pt0) REVERT: G 224 LYS cc_start: 0.6115 (ttpp) cc_final: 0.5701 (pttp) REVERT: G 264 ASN cc_start: 0.6050 (OUTLIER) cc_final: 0.5524 (t0) REVERT: G 380 VAL cc_start: 0.7888 (m) cc_final: 0.7617 (m) REVERT: G 397 ASP cc_start: 0.7016 (m-30) cc_final: 0.6722 (t0) REVERT: G 403 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7132 (ttp-170) REVERT: H 17 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7250 (tmt-80) REVERT: H 75 GLU cc_start: 0.8267 (tp30) cc_final: 0.7773 (tp30) REVERT: H 79 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7984 (ttpt) REVERT: H 184 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6408 (m-30) REVERT: H 192 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7128 (ppp) REVERT: H 213 GLU cc_start: 0.7203 (mp0) cc_final: 0.6865 (mp0) REVERT: H 224 LYS cc_start: 0.6165 (ttpp) cc_final: 0.5869 (pttp) REVERT: H 397 ASP cc_start: 0.7030 (m-30) cc_final: 0.6759 (t0) REVERT: H 403 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7204 (ttp-170) REVERT: H 444 ARG cc_start: 0.8538 (ttp80) cc_final: 0.7405 (tpt90) REVERT: H 483 GLU cc_start: 0.8050 (pt0) cc_final: 0.7504 (mt-10) REVERT: I 12 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.6954 (mtp180) REVERT: I 17 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7160 (tmt-80) REVERT: I 58 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8042 (mm-30) REVERT: I 75 GLU cc_start: 0.8262 (tp30) cc_final: 0.7762 (tp30) REVERT: I 79 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.8020 (ttpt) REVERT: I 110 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.7422 (mtm) REVERT: I 184 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6434 (m-30) REVERT: I 192 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7152 (ppp) REVERT: I 213 GLU cc_start: 0.7185 (mp0) cc_final: 0.6790 (mp0) REVERT: I 224 LYS cc_start: 0.6245 (ttpp) cc_final: 0.5780 (pttp) REVERT: I 380 VAL cc_start: 0.7853 (m) cc_final: 0.7611 (m) REVERT: I 397 ASP cc_start: 0.7028 (m-30) cc_final: 0.6722 (t0) REVERT: I 403 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7208 (ttp-170) REVERT: J 17 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.7250 (tmt-80) REVERT: J 75 GLU cc_start: 0.8262 (tp30) cc_final: 0.7917 (tp30) REVERT: J 79 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7956 (ttpt) REVERT: J 165 MET cc_start: 0.7550 (mtm) cc_final: 0.7165 (mtt) REVERT: J 184 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: J 192 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7164 (ppp) REVERT: J 193 GLN cc_start: 0.7774 (pt0) cc_final: 0.7505 (pt0) REVERT: J 213 GLU cc_start: 0.7158 (mp0) cc_final: 0.6792 (mp0) REVERT: J 224 LYS cc_start: 0.6293 (ttpp) cc_final: 0.5871 (pttp) REVERT: J 397 ASP cc_start: 0.7117 (m-30) cc_final: 0.6833 (t0) REVERT: K 12 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.6851 (mtp180) REVERT: K 17 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7170 (tmt-80) REVERT: K 75 GLU cc_start: 0.8276 (tp30) cc_final: 0.7801 (tp30) REVERT: K 165 MET cc_start: 0.7545 (mtm) cc_final: 0.7331 (mtt) REVERT: K 184 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6388 (m-30) REVERT: K 192 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7171 (ppp) REVERT: K 224 LYS cc_start: 0.6245 (ttpp) cc_final: 0.5918 (pttp) REVERT: K 380 VAL cc_start: 0.7897 (m) cc_final: 0.7654 (m) REVERT: K 397 ASP cc_start: 0.7031 (m-30) cc_final: 0.6778 (t0) REVERT: K 403 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7201 (ttp-170) REVERT: L 12 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.6966 (mtp180) REVERT: L 17 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7283 (tmt-80) REVERT: L 75 GLU cc_start: 0.8307 (tp30) cc_final: 0.7768 (tp30) REVERT: L 79 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7975 (ttpt) REVERT: L 184 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6505 (m-30) REVERT: L 190 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7355 (mm-30) REVERT: L 192 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7077 (ppp) REVERT: L 213 GLU cc_start: 0.7273 (mp0) cc_final: 0.6937 (mp0) REVERT: L 224 LYS cc_start: 0.6167 (ttpp) cc_final: 0.5790 (pttp) REVERT: L 226 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.6320 (tp) REVERT: L 397 ASP cc_start: 0.7033 (m-30) cc_final: 0.6733 (t0) REVERT: M 12 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6855 (mtp180) REVERT: M 17 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7206 (tmt-80) REVERT: M 75 GLU cc_start: 0.8337 (tp30) cc_final: 0.7824 (tp30) REVERT: M 193 GLN cc_start: 0.7667 (pt0) cc_final: 0.7392 (pt0) REVERT: M 213 GLU cc_start: 0.7271 (mp0) cc_final: 0.6824 (mp0) REVERT: M 224 LYS cc_start: 0.6256 (ttpp) cc_final: 0.5904 (pttp) REVERT: M 225 LYS cc_start: 0.7231 (mtmm) cc_final: 0.6601 (mtpp) REVERT: M 397 ASP cc_start: 0.7037 (m-30) cc_final: 0.6765 (t0) REVERT: M 400 HIS cc_start: 0.7529 (m-70) cc_final: 0.7190 (t-90) REVERT: M 403 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7166 (ttp-170) REVERT: M 444 ARG cc_start: 0.8562 (ttp80) cc_final: 0.7359 (tpt90) REVERT: M 483 GLU cc_start: 0.7997 (pt0) cc_final: 0.7400 (mt-10) REVERT: N 12 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7175 (mtp180) REVERT: N 17 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7249 (tmt-80) REVERT: N 75 GLU cc_start: 0.8326 (tp30) cc_final: 0.7780 (tp30) REVERT: N 165 MET cc_start: 0.7514 (mtm) cc_final: 0.7081 (mtt) REVERT: N 184 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6400 (m-30) REVERT: N 193 GLN cc_start: 0.7804 (pt0) cc_final: 0.7534 (pt0) REVERT: N 224 LYS cc_start: 0.6090 (ttpp) cc_final: 0.5689 (pttp) REVERT: N 264 ASN cc_start: 0.6054 (OUTLIER) cc_final: 0.5550 (t0) REVERT: N 320 LYS cc_start: 0.7166 (tptt) cc_final: 0.6901 (tppt) REVERT: N 380 VAL cc_start: 0.7891 (m) cc_final: 0.7620 (m) REVERT: N 397 ASP cc_start: 0.7002 (m-30) cc_final: 0.6715 (t0) REVERT: N 403 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7134 (ttp-170) outliers start: 308 outliers final: 103 residues processed: 1154 average time/residue: 1.4157 time to fit residues: 2046.0731 Evaluate side-chains 1029 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 881 time to evaluate : 4.540 ------------------------------------------------------------------------------- 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 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 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 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 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 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 103 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 397 optimal weight: 20.0000 chunk 440 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 618 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 715 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 450 optimal weight: 0.8980 chunk 673 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN D 365 GLN F 365 GLN G 365 GLN H 365 GLN I 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.208244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129727 restraints weight = 55555.046| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.13 r_work: 0.3254 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 56042 Z= 0.194 Angle : 0.538 7.467 75712 Z= 0.282 Chirality : 0.042 0.154 9142 Planarity : 0.003 0.028 9884 Dihedral : 4.482 43.862 7946 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.44 % Favored : 97.37 % Rotamer: Outliers : 4.93 % Allowed : 24.11 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.10), residues: 7462 helix: 2.25 (0.08), residues: 4228 sheet: -0.18 (0.15), residues: 1106 loop : -0.34 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 2 23 HIS 0.002 0.001 HIS E 400 PHE 0.007 0.001 PHE G 194 TYR 0.010 0.001 TYR C 505 ARG 0.003 0.000 ARG N 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 889 time to evaluate : 4.604 Fit side-chains REVERT: A 17 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7223 (tmt-80) REVERT: A 75 GLU cc_start: 0.8284 (tp30) cc_final: 0.7776 (tp30) REVERT: A 79 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7978 (ttpt) REVERT: A 184 ASP cc_start: 0.6860 (m-30) cc_final: 0.6507 (m-30) REVERT: A 192 MET cc_start: 0.7476 (ppp) cc_final: 0.7147 (ppp) REVERT: A 213 GLU cc_start: 0.7273 (mp0) cc_final: 0.6841 (mp0) REVERT: A 224 LYS cc_start: 0.6204 (ttpp) cc_final: 0.5837 (pttp) REVERT: A 397 ASP cc_start: 0.7047 (m-30) cc_final: 0.6801 (t0) REVERT: A 400 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7160 (t-90) REVERT: A 403 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7118 (ttp-170) REVERT: A 444 ARG cc_start: 0.8533 (ttp80) cc_final: 0.7424 (tpt90) REVERT: A 483 GLU cc_start: 0.7997 (pt0) cc_final: 0.7479 (mt-10) REVERT: B 17 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7154 (tmt-80) REVERT: B 58 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 75 GLU cc_start: 0.8280 (tp30) cc_final: 0.7775 (tp30) REVERT: B 79 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7955 (ttpt) REVERT: B 213 GLU cc_start: 0.7267 (mp0) cc_final: 0.6818 (mp0) REVERT: B 224 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5789 (pttp) REVERT: B 403 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7157 (ttp-170) REVERT: C 12 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.6875 (mtp180) REVERT: C 17 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7231 (tmt-80) REVERT: C 75 GLU cc_start: 0.8245 (tp30) cc_final: 0.7906 (tp30) REVERT: C 79 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7955 (ttpt) REVERT: C 165 MET cc_start: 0.7427 (mtm) cc_final: 0.7147 (mtt) REVERT: C 193 GLN cc_start: 0.7756 (pt0) cc_final: 0.7556 (pt0) REVERT: C 213 GLU cc_start: 0.7249 (mp0) cc_final: 0.6862 (mp0) REVERT: C 224 LYS cc_start: 0.6258 (ttpp) cc_final: 0.5842 (pttp) REVERT: C 397 ASP cc_start: 0.7106 (m-30) cc_final: 0.6840 (t0) REVERT: C 400 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.7214 (t-90) REVERT: D 12 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.6857 (mtp180) REVERT: D 17 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7162 (tmt-80) REVERT: D 75 GLU cc_start: 0.8300 (tp30) cc_final: 0.7832 (tp30) REVERT: D 165 MET cc_start: 0.7491 (mtm) cc_final: 0.7281 (mtt) REVERT: D 224 LYS cc_start: 0.6264 (ttpp) cc_final: 0.5767 (pttp) REVERT: D 397 ASP cc_start: 0.7030 (m-30) cc_final: 0.6747 (t0) REVERT: D 400 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7225 (t-90) REVERT: D 403 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7174 (ttp-170) REVERT: E 12 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.6895 (mtp180) REVERT: E 17 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7294 (tmt-80) REVERT: E 75 GLU cc_start: 0.8313 (tp30) cc_final: 0.7811 (tp30) REVERT: E 79 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7929 (ttpt) REVERT: E 190 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7298 (mm-30) REVERT: E 193 GLN cc_start: 0.7650 (pt0) cc_final: 0.7435 (pt0) REVERT: E 213 GLU cc_start: 0.7271 (mp0) cc_final: 0.6840 (mp0) REVERT: E 224 LYS cc_start: 0.6094 (ttpp) cc_final: 0.5737 (pttp) REVERT: E 397 ASP cc_start: 0.6990 (m-30) cc_final: 0.6722 (t0) REVERT: E 400 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7205 (t-90) REVERT: F 12 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6831 (mtp180) REVERT: F 17 ARG cc_start: 0.8221 (ttp-110) cc_final: 0.7216 (tmt-80) REVERT: F 75 GLU cc_start: 0.8352 (tp30) cc_final: 0.7833 (tp30) REVERT: F 213 GLU cc_start: 0.7291 (mp0) cc_final: 0.6765 (mp0) REVERT: F 224 LYS cc_start: 0.6237 (ttpp) cc_final: 0.5901 (pttp) REVERT: F 397 ASP cc_start: 0.7011 (m-30) cc_final: 0.6756 (t0) REVERT: F 400 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7216 (t-90) REVERT: F 403 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7143 (ttp-170) REVERT: F 444 ARG cc_start: 0.8560 (ttp80) cc_final: 0.7338 (tpt90) REVERT: G 12 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7191 (mtp180) REVERT: G 17 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7241 (tmt-80) REVERT: G 75 GLU cc_start: 0.8333 (tp30) cc_final: 0.7803 (tp30) REVERT: G 165 MET cc_start: 0.7446 (mtp) cc_final: 0.7169 (mtt) REVERT: G 213 GLU cc_start: 0.7327 (mp0) cc_final: 0.6849 (mp0) REVERT: G 224 LYS cc_start: 0.6165 (ttpp) cc_final: 0.5733 (pttp) REVERT: G 264 ASN cc_start: 0.6086 (OUTLIER) cc_final: 0.5854 (m-40) REVERT: G 397 ASP cc_start: 0.6979 (m-30) cc_final: 0.6710 (t0) REVERT: G 400 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.7251 (t-90) REVERT: G 403 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7141 (ttp-170) REVERT: H 17 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7228 (tmt-80) REVERT: H 75 GLU cc_start: 0.8275 (tp30) cc_final: 0.7766 (tp30) REVERT: H 79 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7971 (ttpt) REVERT: H 184 ASP cc_start: 0.6874 (m-30) cc_final: 0.6518 (m-30) REVERT: H 192 MET cc_start: 0.7461 (ppp) cc_final: 0.7130 (ppp) REVERT: H 213 GLU cc_start: 0.7270 (mp0) cc_final: 0.6843 (mp0) REVERT: H 224 LYS cc_start: 0.6184 (ttpp) cc_final: 0.5822 (pttp) REVERT: H 397 ASP cc_start: 0.7051 (m-30) cc_final: 0.6804 (t0) REVERT: H 400 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7155 (t-90) REVERT: H 403 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.7115 (ttp-170) REVERT: H 444 ARG cc_start: 0.8542 (ttp80) cc_final: 0.7426 (tpt90) REVERT: H 483 GLU cc_start: 0.8003 (pt0) cc_final: 0.7476 (mt-10) REVERT: I 12 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6911 (mtp180) REVERT: I 17 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7156 (tmt-80) REVERT: I 58 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8065 (mm-30) REVERT: I 75 GLU cc_start: 0.8312 (tp30) cc_final: 0.7807 (tp30) REVERT: I 79 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7967 (ttpt) REVERT: I 192 MET cc_start: 0.7467 (ppp) cc_final: 0.7141 (ppp) REVERT: I 213 GLU cc_start: 0.7225 (mp0) cc_final: 0.6800 (mp0) REVERT: I 224 LYS cc_start: 0.6183 (ttpp) cc_final: 0.5779 (pttp) REVERT: I 403 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7158 (ttp-170) REVERT: J 12 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.6899 (mtp180) REVERT: J 17 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7235 (tmt-80) REVERT: J 75 GLU cc_start: 0.8241 (tp30) cc_final: 0.7902 (tp30) REVERT: J 79 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7949 (ttpt) REVERT: J 165 MET cc_start: 0.7385 (mtm) cc_final: 0.7103 (mtt) REVERT: J 193 GLN cc_start: 0.7750 (pt0) cc_final: 0.7545 (pt0) REVERT: J 213 GLU cc_start: 0.7262 (mp0) cc_final: 0.6816 (mp0) REVERT: J 224 LYS cc_start: 0.6275 (ttpp) cc_final: 0.5829 (pttp) REVERT: J 397 ASP cc_start: 0.7096 (m-30) cc_final: 0.6828 (t0) REVERT: J 400 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7205 (t-90) REVERT: K 12 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.6844 (mtp180) REVERT: K 17 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7177 (tmt-80) REVERT: K 75 GLU cc_start: 0.8307 (tp30) cc_final: 0.7839 (tp30) REVERT: K 213 GLU cc_start: 0.7373 (mp0) cc_final: 0.6924 (mp0) REVERT: K 224 LYS cc_start: 0.6259 (ttpp) cc_final: 0.5750 (pttp) REVERT: K 397 ASP cc_start: 0.7030 (m-30) cc_final: 0.6749 (t0) REVERT: K 400 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7230 (t-90) REVERT: K 403 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7178 (ttp-170) REVERT: L 12 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.6909 (mtp180) REVERT: L 17 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7298 (tmt-80) REVERT: L 75 GLU cc_start: 0.8302 (tp30) cc_final: 0.7831 (tp30) REVERT: L 79 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7959 (ttpt) REVERT: L 190 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7241 (mm-30) REVERT: L 224 LYS cc_start: 0.6151 (ttpp) cc_final: 0.5795 (pttp) REVERT: L 397 ASP cc_start: 0.7004 (m-30) cc_final: 0.6728 (t0) REVERT: L 400 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.7210 (t-90) REVERT: M 12 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6839 (mtp180) REVERT: M 17 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7224 (tmt-80) REVERT: M 75 GLU cc_start: 0.8332 (tp30) cc_final: 0.7824 (tp30) REVERT: M 79 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7862 (mtpt) REVERT: M 224 LYS cc_start: 0.6240 (ttpp) cc_final: 0.5898 (pttp) REVERT: M 397 ASP cc_start: 0.6995 (m-30) cc_final: 0.6736 (t0) REVERT: M 400 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7229 (t-90) REVERT: M 403 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7073 (ttp-170) REVERT: M 444 ARG cc_start: 0.8560 (ttp80) cc_final: 0.7337 (tpt90) REVERT: M 483 GLU cc_start: 0.7969 (pt0) cc_final: 0.7397 (mt-10) REVERT: N 12 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7188 (mtp180) REVERT: N 17 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7242 (tmt-80) REVERT: N 75 GLU cc_start: 0.8332 (tp30) cc_final: 0.7804 (tp30) REVERT: N 165 MET cc_start: 0.7453 (mtp) cc_final: 0.7199 (mtt) REVERT: N 224 LYS cc_start: 0.6142 (ttpp) cc_final: 0.5622 (pttp) REVERT: N 320 LYS cc_start: 0.7214 (tptt) cc_final: 0.6915 (tppt) REVERT: N 397 ASP cc_start: 0.6990 (m-30) cc_final: 0.6727 (t0) REVERT: N 400 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7284 (t-90) REVERT: N 403 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7144 (ttp-170) outliers start: 287 outliers final: 137 residues processed: 1088 average time/residue: 1.3637 time to fit residues: 1874.9584 Evaluate side-chains 1020 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 850 time to evaluate : 4.464 ------------------------------------------------------------------------------- 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 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 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 176 VAL Chi-restraints excluded: chain C residue 178 ASP 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 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 153 SER Chi-restraints excluded: chain E residue 176 VAL 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 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 153 SER Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 264 ASN Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 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 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 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 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 176 VAL Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 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 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 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 158 optimal weight: 4.9990 chunk 572 optimal weight: 5.9990 chunk 318 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 475 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 264 optimal weight: 0.0170 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN C 365 GLN D 365 GLN F 365 GLN G 318 GLN G 365 GLN I 365 GLN J 365 GLN K 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.208192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128188 restraints weight = 55164.725| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.71 r_work: 0.3297 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56042 Z= 0.178 Angle : 0.526 7.197 75712 Z= 0.276 Chirality : 0.041 0.151 9142 Planarity : 0.003 0.028 9884 Dihedral : 4.488 52.052 7940 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.88 % Favored : 96.93 % Rotamer: Outliers : 5.24 % Allowed : 23.70 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.10), residues: 7462 helix: 2.28 (0.08), residues: 4228 sheet: -0.18 (0.16), residues: 1106 loop : -0.38 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 23 HIS 0.002 0.001 HIS L 400 PHE 0.010 0.001 PHE 2 25 TYR 0.010 0.001 TYR C 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 1189 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 305 poor density : 884 time to evaluate : 4.744 Fit side-chains REVERT: A 17 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7008 (tmt-80) REVERT: A 75 GLU cc_start: 0.8106 (tp30) cc_final: 0.7581 (tp30) REVERT: A 79 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7842 (ttpt) REVERT: A 213 GLU cc_start: 0.7257 (mp0) cc_final: 0.6769 (mp0) REVERT: A 224 LYS cc_start: 0.6179 (ttpp) cc_final: 0.5769 (pttp) REVERT: A 306 MET cc_start: 0.4517 (mmp) cc_final: 0.4275 (mmp) REVERT: A 397 ASP cc_start: 0.6983 (m-30) cc_final: 0.6725 (t0) REVERT: A 400 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.7100 (t-90) REVERT: A 403 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.6965 (ttp-170) REVERT: A 444 ARG cc_start: 0.8433 (ttp80) cc_final: 0.7259 (tpt90) REVERT: A 483 GLU cc_start: 0.7855 (pt0) cc_final: 0.7343 (mt-10) REVERT: B 17 ARG cc_start: 0.8045 (ttp-110) cc_final: 0.6941 (tmt-80) REVERT: B 58 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7978 (mm-30) REVERT: B 75 GLU cc_start: 0.8144 (tp30) cc_final: 0.7619 (tp30) REVERT: B 79 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7825 (ttpt) REVERT: B 213 GLU cc_start: 0.7210 (mp0) cc_final: 0.6751 (mp0) REVERT: B 224 LYS cc_start: 0.6122 (ttpp) cc_final: 0.5802 (pttp) REVERT: B 400 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7116 (t-90) REVERT: B 403 ARG cc_start: 0.7432 (ttm-80) cc_final: 0.7049 (ttp-170) REVERT: C 12 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.6763 (mtp180) REVERT: C 17 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7025 (tmt-80) REVERT: C 75 GLU cc_start: 0.8107 (tp30) cc_final: 0.7764 (tp30) REVERT: C 79 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7819 (ttpt) REVERT: C 165 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7048 (mtt) REVERT: C 213 GLU cc_start: 0.7187 (mp0) cc_final: 0.6774 (mp0) REVERT: C 224 LYS cc_start: 0.6213 (ttpp) cc_final: 0.5780 (pttp) REVERT: C 236 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5890 (mt) REVERT: C 400 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.7121 (t-90) REVERT: D 12 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6700 (mtp180) REVERT: D 17 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.6961 (tmt-80) REVERT: D 75 GLU cc_start: 0.8138 (tp30) cc_final: 0.7643 (tp30) REVERT: D 213 GLU cc_start: 0.7287 (mp0) cc_final: 0.6864 (mp0) REVERT: D 224 LYS cc_start: 0.6182 (ttpp) cc_final: 0.5691 (pttp) REVERT: D 400 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.7147 (t-90) REVERT: D 403 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.7043 (ttp-170) REVERT: E 12 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.6747 (mtp180) REVERT: E 17 ARG cc_start: 0.8122 (ttp-110) cc_final: 0.7088 (tmt-80) REVERT: E 75 GLU cc_start: 0.8135 (tp30) cc_final: 0.7654 (tp30) REVERT: E 79 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7768 (ttpt) REVERT: E 213 GLU cc_start: 0.7202 (mp0) cc_final: 0.6789 (mp0) REVERT: E 224 LYS cc_start: 0.6031 (ttpp) cc_final: 0.5644 (pttp) REVERT: E 236 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5736 (mt) REVERT: E 283 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.5773 (mpp80) REVERT: E 306 MET cc_start: 0.4619 (mmp) cc_final: 0.4342 (mmp) REVERT: E 397 ASP cc_start: 0.6918 (m-30) cc_final: 0.6652 (t0) REVERT: E 400 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7092 (t-90) REVERT: F 12 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6693 (mtp180) REVERT: F 17 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7015 (tmt-80) REVERT: F 75 GLU cc_start: 0.8159 (tp30) cc_final: 0.7637 (tp30) REVERT: F 213 GLU cc_start: 0.7282 (mp0) cc_final: 0.6752 (mp0) REVERT: F 224 LYS cc_start: 0.6231 (ttpp) cc_final: 0.5813 (pttp) REVERT: F 306 MET cc_start: 0.4404 (mmp) cc_final: 0.4204 (mmp) REVERT: F 397 ASP cc_start: 0.6934 (m-30) cc_final: 0.6661 (t0) REVERT: F 400 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.7101 (t-90) REVERT: F 403 ARG cc_start: 0.7332 (ttm-80) cc_final: 0.6876 (ttp-170) REVERT: F 444 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7149 (tpt90) REVERT: G 12 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7021 (mtp180) REVERT: G 17 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7031 (tmt-80) REVERT: G 75 GLU cc_start: 0.8170 (tp30) cc_final: 0.7581 (tp30) REVERT: G 79 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7611 (mtpt) REVERT: G 165 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7089 (mtt) REVERT: G 213 GLU cc_start: 0.7247 (mp0) cc_final: 0.6726 (mp0) REVERT: G 224 LYS cc_start: 0.6169 (ttpp) cc_final: 0.5766 (pttp) REVERT: G 397 ASP cc_start: 0.6953 (m-30) cc_final: 0.6684 (t0) REVERT: G 400 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.7182 (t-90) REVERT: G 403 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.7009 (ttp-170) REVERT: H 17 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7021 (tmt-80) REVERT: H 75 GLU cc_start: 0.8092 (tp30) cc_final: 0.7564 (tp30) REVERT: H 79 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7841 (ttpt) REVERT: H 213 GLU cc_start: 0.7254 (mp0) cc_final: 0.6775 (mp0) REVERT: H 224 LYS cc_start: 0.6175 (ttpp) cc_final: 0.5759 (pttp) REVERT: H 306 MET cc_start: 0.4508 (mmp) cc_final: 0.4264 (mmp) REVERT: H 397 ASP cc_start: 0.6976 (m-30) cc_final: 0.6718 (t0) REVERT: H 400 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7095 (t-90) REVERT: H 403 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6965 (ttp-170) REVERT: H 444 ARG cc_start: 0.8429 (ttp80) cc_final: 0.7250 (tpt90) REVERT: H 483 GLU cc_start: 0.7857 (pt0) cc_final: 0.7347 (mt-10) REVERT: I 12 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.6760 (mtp180) REVERT: I 17 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.6948 (tmt-80) REVERT: I 58 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7993 (mm-30) REVERT: I 75 GLU cc_start: 0.8157 (tp30) cc_final: 0.7628 (tp30) REVERT: I 79 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7837 (ttpt) REVERT: I 224 LYS cc_start: 0.6130 (ttpp) cc_final: 0.5821 (pttp) REVERT: I 400 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.7113 (t-90) REVERT: I 403 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.7052 (ttp-170) REVERT: J 12 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6758 (mtp180) REVERT: J 17 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7027 (tmt-80) REVERT: J 75 GLU cc_start: 0.8110 (tp30) cc_final: 0.7766 (tp30) REVERT: J 79 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7812 (ttpt) REVERT: J 165 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.7025 (mtt) REVERT: J 213 GLU cc_start: 0.7209 (mp0) cc_final: 0.6784 (mp0) REVERT: J 224 LYS cc_start: 0.6224 (ttpp) cc_final: 0.5789 (pttp) REVERT: J 236 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5877 (mt) REVERT: J 400 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7127 (t-90) REVERT: K 12 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.6703 (mtp180) REVERT: K 17 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.6957 (tmt-80) REVERT: K 75 GLU cc_start: 0.8139 (tp30) cc_final: 0.7649 (tp30) REVERT: K 213 GLU cc_start: 0.7293 (mp0) cc_final: 0.6859 (mp0) REVERT: K 224 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5685 (pttp) REVERT: K 397 ASP cc_start: 0.6995 (m-30) cc_final: 0.6709 (t0) REVERT: K 400 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: K 403 ARG cc_start: 0.7412 (ttm-80) cc_final: 0.6997 (ttp-170) REVERT: L 12 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6748 (mtp180) REVERT: L 17 ARG cc_start: 0.8115 (ttp-110) cc_final: 0.7084 (tmt-80) REVERT: L 75 GLU cc_start: 0.8151 (tp30) cc_final: 0.7671 (tp30) REVERT: L 79 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7806 (ttpt) REVERT: L 213 GLU cc_start: 0.7246 (mp0) cc_final: 0.6825 (mp0) REVERT: L 224 LYS cc_start: 0.6039 (ttpp) cc_final: 0.5623 (pttp) REVERT: L 236 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5766 (mt) REVERT: L 283 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.5770 (mpp80) REVERT: L 306 MET cc_start: 0.4616 (mmp) cc_final: 0.4379 (mmp) REVERT: L 397 ASP cc_start: 0.6947 (m-30) cc_final: 0.6681 (t0) REVERT: L 400 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7103 (t-90) REVERT: M 12 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.6686 (mtp180) REVERT: M 17 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7018 (tmt-80) REVERT: M 75 GLU cc_start: 0.8157 (tp30) cc_final: 0.7634 (tp30) REVERT: M 213 GLU cc_start: 0.7268 (mp0) cc_final: 0.6696 (mp0) REVERT: M 224 LYS cc_start: 0.6230 (ttpp) cc_final: 0.5808 (pttp) REVERT: M 400 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7116 (t-90) REVERT: M 403 ARG cc_start: 0.7370 (ttm-80) cc_final: 0.6918 (ttp-170) REVERT: M 444 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7163 (tpt90) REVERT: M 483 GLU cc_start: 0.7829 (pt0) cc_final: 0.7250 (mt-10) REVERT: N 12 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7019 (mtp180) REVERT: N 17 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7032 (tmt-80) REVERT: N 75 GLU cc_start: 0.8168 (tp30) cc_final: 0.7581 (tp30) REVERT: N 79 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7602 (mtpt) REVERT: N 213 GLU cc_start: 0.7283 (mp0) cc_final: 0.6801 (mp0) REVERT: N 224 LYS cc_start: 0.6061 (ttpp) cc_final: 0.5612 (pttp) REVERT: N 320 LYS cc_start: 0.7235 (tptt) cc_final: 0.6913 (tppt) REVERT: N 397 ASP cc_start: 0.6960 (m-30) cc_final: 0.6701 (t0) REVERT: N 400 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.7195 (t-90) REVERT: N 403 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.7006 (ttp-170) outliers start: 305 outliers final: 143 residues processed: 1109 average time/residue: 1.3306 time to fit residues: 1872.9500 Evaluate side-chains 1052 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 865 time to evaluate : 4.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 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 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 299 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain E residue 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 86 ASP Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 368 VAL Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 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 60 GLU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain 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 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 86 ASP 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 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 155 optimal weight: 4.9990 chunk 678 optimal weight: 2.9990 chunk 389 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 524 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 446 optimal weight: 20.0000 chunk 132 optimal weight: 0.4980 chunk 258 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 356 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.207605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126847 restraints weight = 55393.672| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.71 r_work: 0.3294 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 56042 Z= 0.212 Angle : 0.536 7.753 75712 Z= 0.281 Chirality : 0.042 0.152 9142 Planarity : 0.003 0.030 9884 Dihedral : 4.666 59.687 7938 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.84 % Favored : 96.97 % Rotamer: Outliers : 5.82 % Allowed : 23.32 % 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: 1.69 (0.10), residues: 7462 helix: 2.25 (0.08), residues: 4228 sheet: -0.19 (0.16), residues: 1106 loop : -0.42 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 1 18 HIS 0.003 0.001 HIS 1 26 PHE 0.007 0.001 PHE G 194 TYR 0.011 0.001 TYR J 505 ARG 0.005 0.000 ARG H 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 339 poor density : 876 time to evaluate : 4.580 Fit side-chains REVERT: A 17 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7156 (tmt-80) REVERT: A 75 GLU cc_start: 0.8199 (tp30) cc_final: 0.7700 (tp30) REVERT: A 79 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8054 (ttpt) REVERT: A 213 GLU cc_start: 0.7339 (mp0) cc_final: 0.6859 (mp0) REVERT: A 224 LYS cc_start: 0.6223 (ttpp) cc_final: 0.5815 (pttp) REVERT: A 306 MET cc_start: 0.4469 (mmp) cc_final: 0.4226 (mmp) REVERT: A 400 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.7108 (t-90) REVERT: A 403 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.7028 (ttp-170) REVERT: A 444 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7394 (tpt90) REVERT: A 483 GLU cc_start: 0.7876 (pt0) cc_final: 0.7434 (mt-10) REVERT: B 17 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7163 (tmt-80) REVERT: B 58 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8072 (mm-30) REVERT: B 75 GLU cc_start: 0.8209 (tp30) cc_final: 0.7703 (tp30) REVERT: B 79 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8014 (ttpt) REVERT: B 224 LYS cc_start: 0.6180 (ttpp) cc_final: 0.5853 (pttp) REVERT: B 306 MET cc_start: 0.4369 (mmp) cc_final: 0.4139 (mmp) REVERT: B 400 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.7131 (t-90) REVERT: B 403 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.7125 (ttp-170) REVERT: C 12 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.6849 (mtp180) REVERT: C 17 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7162 (tmt-80) REVERT: C 75 GLU cc_start: 0.8184 (tp30) cc_final: 0.7867 (tp30) REVERT: C 79 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7998 (ttpt) REVERT: C 165 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.7012 (mtt) REVERT: C 213 GLU cc_start: 0.7246 (mp0) cc_final: 0.6784 (mp0) REVERT: C 224 LYS cc_start: 0.6272 (ttpp) cc_final: 0.5840 (pttp) REVERT: C 236 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5870 (mt) REVERT: C 306 MET cc_start: 0.4364 (mmp) cc_final: 0.4141 (mmp) REVERT: C 400 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7184 (t-90) REVERT: D 12 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.6872 (mtp180) REVERT: D 17 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7136 (tmt-80) REVERT: D 75 GLU cc_start: 0.8198 (tp30) cc_final: 0.7790 (tp30) REVERT: D 193 GLN cc_start: 0.7594 (pt0) cc_final: 0.7267 (pt0) REVERT: D 213 GLU cc_start: 0.7365 (mp0) cc_final: 0.6881 (mp0) REVERT: D 224 LYS cc_start: 0.6210 (ttpp) cc_final: 0.5735 (pttp) REVERT: D 306 MET cc_start: 0.4403 (mmp) cc_final: 0.4166 (mmp) REVERT: D 400 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: D 403 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.7067 (ttp-170) REVERT: E 12 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6893 (mtp180) REVERT: E 17 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7224 (tmt-80) REVERT: E 75 GLU cc_start: 0.8247 (tp30) cc_final: 0.7820 (tp30) REVERT: E 79 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8021 (ttpt) REVERT: E 184 ASP cc_start: 0.6994 (m-30) cc_final: 0.6740 (m-30) REVERT: E 213 GLU cc_start: 0.7292 (mp0) cc_final: 0.6838 (mp0) REVERT: E 224 LYS cc_start: 0.6161 (ttpp) cc_final: 0.5785 (pttp) REVERT: E 236 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5790 (mt) REVERT: E 283 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.5922 (mpp80) REVERT: E 400 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.7162 (t-90) REVERT: F 12 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.6818 (mtp180) REVERT: F 17 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7179 (tmt-80) REVERT: F 75 GLU cc_start: 0.8190 (tp30) cc_final: 0.7679 (tp30) REVERT: F 79 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7948 (mtpt) REVERT: F 213 GLU cc_start: 0.7303 (mp0) cc_final: 0.6735 (mp0) REVERT: F 224 LYS cc_start: 0.6294 (ttpp) cc_final: 0.5909 (pttp) REVERT: F 264 ASN cc_start: 0.5894 (OUTLIER) cc_final: 0.5624 (t0) REVERT: F 306 MET cc_start: 0.4486 (mmp) cc_final: 0.4191 (mmp) REVERT: F 400 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.7208 (t-90) REVERT: F 403 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.6903 (ttp-170) REVERT: G 12 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7135 (mtp180) REVERT: G 17 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7200 (tmt-80) REVERT: G 75 GLU cc_start: 0.8243 (tp30) cc_final: 0.7689 (tp30) REVERT: G 79 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7793 (mtpt) REVERT: G 224 LYS cc_start: 0.6170 (ttpp) cc_final: 0.5731 (pttp) REVERT: G 400 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.7267 (t-90) REVERT: G 403 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.7085 (ttp-170) REVERT: H 17 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7154 (tmt-80) REVERT: H 75 GLU cc_start: 0.8188 (tp30) cc_final: 0.7688 (tp30) REVERT: H 79 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8046 (ttpt) REVERT: H 213 GLU cc_start: 0.7376 (mp0) cc_final: 0.6887 (mp0) REVERT: H 224 LYS cc_start: 0.6213 (ttpp) cc_final: 0.5805 (pttp) REVERT: H 306 MET cc_start: 0.4473 (mmp) cc_final: 0.4228 (mmp) REVERT: H 400 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.7105 (t-90) REVERT: H 403 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.7031 (ttp-170) REVERT: H 444 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7394 (tpt90) REVERT: H 483 GLU cc_start: 0.7874 (pt0) cc_final: 0.7434 (mt-10) REVERT: I 12 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.6837 (mtp180) REVERT: I 17 ARG cc_start: 0.8163 (ttp-110) cc_final: 0.7164 (tmt-80) REVERT: I 58 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8073 (mm-30) REVERT: I 75 GLU cc_start: 0.8211 (tp30) cc_final: 0.7703 (tp30) REVERT: I 79 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8017 (ttpt) REVERT: I 224 LYS cc_start: 0.6178 (ttpp) cc_final: 0.5860 (pttp) REVERT: I 306 MET cc_start: 0.4374 (mmp) cc_final: 0.4144 (mmp) REVERT: I 400 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.7122 (t-90) REVERT: I 403 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7125 (ttp-170) REVERT: J 12 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.6841 (mtp180) REVERT: J 17 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7162 (tmt-80) REVERT: J 75 GLU cc_start: 0.8185 (tp30) cc_final: 0.7863 (tp30) REVERT: J 79 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7995 (ttpt) REVERT: J 165 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.7011 (mtt) REVERT: J 213 GLU cc_start: 0.7279 (mp0) cc_final: 0.6960 (mp0) REVERT: J 224 LYS cc_start: 0.6239 (ttpp) cc_final: 0.5793 (pttp) REVERT: J 236 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5860 (mt) REVERT: J 306 MET cc_start: 0.4406 (mmp) cc_final: 0.4179 (mmp) REVERT: J 321 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6614 (ttt-90) REVERT: J 400 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7179 (t-90) REVERT: K 12 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.6870 (mtp180) REVERT: K 17 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7131 (tmt-80) REVERT: K 75 GLU cc_start: 0.8183 (tp30) cc_final: 0.7775 (tp30) REVERT: K 193 GLN cc_start: 0.7627 (pt0) cc_final: 0.7301 (pt0) REVERT: K 213 GLU cc_start: 0.7378 (mp0) cc_final: 0.6901 (mp0) REVERT: K 224 LYS cc_start: 0.6203 (ttpp) cc_final: 0.5725 (pttp) REVERT: K 306 MET cc_start: 0.4418 (mmp) cc_final: 0.4179 (mmp) REVERT: K 400 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7218 (t-90) REVERT: K 403 ARG cc_start: 0.7447 (ttm-80) cc_final: 0.7032 (ttp-170) REVERT: L 12 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.6895 (mtp180) REVERT: L 17 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7232 (tmt-80) REVERT: L 75 GLU cc_start: 0.8247 (tp30) cc_final: 0.7822 (tp30) REVERT: L 79 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8012 (ttpt) REVERT: L 193 GLN cc_start: 0.7629 (pt0) cc_final: 0.7349 (pt0) REVERT: L 213 GLU cc_start: 0.7411 (mp0) cc_final: 0.6988 (mp0) REVERT: L 224 LYS cc_start: 0.6151 (ttpp) cc_final: 0.5752 (pttp) REVERT: L 236 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5838 (mt) REVERT: L 283 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5933 (mpp80) REVERT: L 400 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7152 (t-90) REVERT: M 12 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.6803 (mtp180) REVERT: M 17 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7167 (tmt-80) REVERT: M 75 GLU cc_start: 0.8187 (tp30) cc_final: 0.7677 (tp30) REVERT: M 79 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7939 (mtpt) REVERT: M 213 GLU cc_start: 0.7314 (mp0) cc_final: 0.6744 (mp0) REVERT: M 224 LYS cc_start: 0.6271 (ttpp) cc_final: 0.5882 (pttp) REVERT: M 264 ASN cc_start: 0.5847 (OUTLIER) cc_final: 0.5568 (t0) REVERT: M 400 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7201 (t-90) REVERT: M 403 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.6929 (ttp-170) REVERT: M 483 GLU cc_start: 0.7861 (pt0) cc_final: 0.7383 (mt-10) REVERT: N 12 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7133 (mtp180) REVERT: N 17 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7198 (tmt-80) REVERT: N 75 GLU cc_start: 0.8240 (tp30) cc_final: 0.7687 (tp30) REVERT: N 79 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7794 (mtpt) REVERT: N 213 GLU cc_start: 0.7358 (mp0) cc_final: 0.6844 (mp0) REVERT: N 224 LYS cc_start: 0.6134 (ttpp) cc_final: 0.5750 (pttp) REVERT: N 320 LYS cc_start: 0.7273 (tptt) cc_final: 0.6948 (tppt) REVERT: N 321 ARG cc_start: 0.7382 (ttm-80) cc_final: 0.7114 (ttt90) REVERT: N 400 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7269 (t-90) REVERT: N 403 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.7055 (ttp-170) outliers start: 339 outliers final: 172 residues processed: 1104 average time/residue: 1.3383 time to fit residues: 1887.7556 Evaluate side-chains 1082 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 862 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 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 60 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 176 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 E residue 12 ARG Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 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 86 ASP 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 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 247 LEU 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 86 ASP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain 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 86 ASP 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 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 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 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 321 ARG Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain 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 86 ASP Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 176 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 L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 153 SER Chi-restraints excluded: chain M residue 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 320 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 86 ASP Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain P residue 26 HIS Chi-restraints excluded: chain W residue 26 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 608 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 531 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 623 optimal weight: 3.9990 chunk 328 optimal weight: 9.9990 chunk 606 optimal weight: 7.9990 chunk 696 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 318 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.206053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125187 restraints weight = 55204.718| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.70 r_work: 0.3266 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 56042 Z= 0.259 Angle : 0.570 8.406 75712 Z= 0.296 Chirality : 0.043 0.155 9142 Planarity : 0.004 0.031 9884 Dihedral : 4.660 53.992 7936 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.68 % Favored : 97.13 % Rotamer: Outliers : 6.37 % Allowed : 22.65 % Favored : 70.98 % 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: 1.47 (0.10), residues: 7462 helix: 2.13 (0.08), residues: 4228 sheet: -0.98 (0.18), residues: 826 loop : -0.35 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 18 HIS 0.003 0.002 HIS L 400 PHE 0.006 0.001 PHE G 194 TYR 0.013 0.001 TYR C 505 ARG 0.004 0.000 ARG B 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 1260 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 371 poor density : 889 time to evaluate : 4.583 Fit side-chains REVERT: A 17 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7203 (tmt-80) REVERT: A 75 GLU cc_start: 0.8234 (tp30) cc_final: 0.7800 (tp30) REVERT: A 79 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8051 (ttpt) REVERT: A 184 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: A 193 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: A 213 GLU cc_start: 0.7365 (mp0) cc_final: 0.6864 (mp0) REVERT: A 224 LYS cc_start: 0.6158 (ttpp) cc_final: 0.5774 (pttp) REVERT: A 306 MET cc_start: 0.4505 (mmp) cc_final: 0.4169 (mmp) REVERT: A 400 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7081 (t-90) REVERT: A 403 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.7020 (ttp-170) REVERT: A 483 GLU cc_start: 0.7898 (pt0) cc_final: 0.7451 (mt-10) REVERT: B 17 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7167 (tmt-80) REVERT: B 58 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8065 (mm-30) REVERT: B 75 GLU cc_start: 0.8209 (tp30) cc_final: 0.7795 (tp30) REVERT: B 79 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7882 (mtmm) REVERT: B 184 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: B 224 LYS cc_start: 0.6136 (ttpp) cc_final: 0.5716 (pttp) REVERT: B 306 MET cc_start: 0.4170 (mmp) cc_final: 0.3816 (mmp) REVERT: B 400 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7107 (t-90) REVERT: B 403 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7057 (ttp-170) REVERT: C 12 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6896 (mtp180) REVERT: C 17 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7210 (tmt-80) REVERT: C 75 GLU cc_start: 0.8205 (tp30) cc_final: 0.7768 (tp30) REVERT: C 79 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7962 (ttpt) REVERT: C 165 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7023 (mtt) REVERT: C 184 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6776 (m-30) REVERT: C 193 GLN cc_start: 0.7682 (pt0) cc_final: 0.7433 (pt0) REVERT: C 213 GLU cc_start: 0.7238 (mp0) cc_final: 0.6778 (mp0) REVERT: C 224 LYS cc_start: 0.6295 (ttpp) cc_final: 0.5847 (pttp) REVERT: C 236 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5859 (mt) REVERT: C 306 MET cc_start: 0.4323 (mmp) cc_final: 0.4021 (mmp) REVERT: C 400 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.7164 (t-90) REVERT: D 12 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.6856 (mtp180) REVERT: D 17 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7166 (tmt-80) REVERT: D 75 GLU cc_start: 0.8206 (tp30) cc_final: 0.7804 (tp30) REVERT: D 184 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: D 193 GLN cc_start: 0.7588 (pt0) cc_final: 0.7250 (pt0) REVERT: D 213 GLU cc_start: 0.7371 (mp0) cc_final: 0.6842 (mp0) REVERT: D 224 LYS cc_start: 0.6243 (ttpp) cc_final: 0.5773 (pttp) REVERT: D 306 MET cc_start: 0.4361 (mmp) cc_final: 0.4048 (mmp) REVERT: D 400 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7163 (t-90) REVERT: D 403 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.6977 (ttp-110) REVERT: E 12 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.6949 (mtp180) REVERT: E 17 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7234 (tmt-80) REVERT: E 75 GLU cc_start: 0.8281 (tp30) cc_final: 0.7862 (tp30) REVERT: E 79 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8024 (ttpt) REVERT: E 193 GLN cc_start: 0.7603 (pt0) cc_final: 0.7303 (pt0) REVERT: E 224 LYS cc_start: 0.6141 (ttpp) cc_final: 0.5778 (pttp) REVERT: E 236 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5779 (mt) REVERT: E 283 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.5834 (mpp80) REVERT: E 306 MET cc_start: 0.4586 (mmp) cc_final: 0.4184 (mmp) REVERT: E 400 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: F 12 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6818 (mtp180) REVERT: F 17 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7193 (tmt-80) REVERT: F 75 GLU cc_start: 0.8215 (tp30) cc_final: 0.7786 (tp30) REVERT: F 184 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6688 (m-30) REVERT: F 193 GLN cc_start: 0.7647 (pt0) cc_final: 0.7412 (pt0) REVERT: F 213 GLU cc_start: 0.7271 (mp0) cc_final: 0.6738 (mp0) REVERT: F 224 LYS cc_start: 0.6312 (ttpp) cc_final: 0.6039 (pttp) REVERT: F 264 ASN cc_start: 0.5910 (OUTLIER) cc_final: 0.5637 (t0) REVERT: F 306 MET cc_start: 0.4462 (mmp) cc_final: 0.4085 (mmp) REVERT: F 400 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7166 (t-90) REVERT: F 403 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7179 (mtt-85) REVERT: G 12 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7136 (mtp180) REVERT: G 17 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7215 (tmt-80) REVERT: G 75 GLU cc_start: 0.8263 (tp30) cc_final: 0.7726 (tp30) REVERT: G 79 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7809 (mtpt) REVERT: G 184 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: G 224 LYS cc_start: 0.6195 (ttpp) cc_final: 0.5762 (pttp) REVERT: G 400 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7251 (t-90) REVERT: G 403 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7046 (ttp-170) REVERT: H 17 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7203 (tmt-80) REVERT: H 75 GLU cc_start: 0.8237 (tp30) cc_final: 0.7805 (tp30) REVERT: H 79 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8047 (ttpt) REVERT: H 184 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: H 193 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7348 (pt0) REVERT: H 213 GLU cc_start: 0.7367 (mp0) cc_final: 0.6866 (mp0) REVERT: H 224 LYS cc_start: 0.6149 (ttpp) cc_final: 0.5765 (pttp) REVERT: H 306 MET cc_start: 0.4506 (mmp) cc_final: 0.4166 (mmp) REVERT: H 400 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7091 (t-90) REVERT: H 403 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7023 (ttp-170) REVERT: H 483 GLU cc_start: 0.7892 (pt0) cc_final: 0.7449 (mt-10) REVERT: I 12 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.6780 (mtp180) REVERT: I 17 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7178 (tmt-80) REVERT: I 58 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8058 (mm-30) REVERT: I 75 GLU cc_start: 0.8222 (tp30) cc_final: 0.7806 (tp30) REVERT: I 79 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7882 (mtmm) REVERT: I 224 LYS cc_start: 0.6156 (ttpp) cc_final: 0.5830 (pttp) REVERT: I 306 MET cc_start: 0.4195 (mmp) cc_final: 0.3844 (mmp) REVERT: I 400 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7131 (t-90) REVERT: I 403 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.7058 (ttp-170) REVERT: J 12 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.6905 (mtp180) REVERT: J 17 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7213 (tmt-80) REVERT: J 75 GLU cc_start: 0.8208 (tp30) cc_final: 0.7774 (tp30) REVERT: J 79 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7965 (ttpt) REVERT: J 165 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.7008 (mtt) REVERT: J 184 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: J 193 GLN cc_start: 0.7686 (pt0) cc_final: 0.7472 (pt0) REVERT: J 224 LYS cc_start: 0.6266 (ttpp) cc_final: 0.5802 (pttp) REVERT: J 236 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5849 (mt) REVERT: J 306 MET cc_start: 0.4301 (mmp) cc_final: 0.3999 (mmp) REVERT: J 321 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6579 (ttt-90) REVERT: J 400 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7190 (t-90) REVERT: K 12 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.6860 (mtp180) REVERT: K 17 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7156 (tmt-80) REVERT: K 75 GLU cc_start: 0.8205 (tp30) cc_final: 0.7802 (tp30) REVERT: K 184 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: K 193 GLN cc_start: 0.7592 (pt0) cc_final: 0.7260 (pt0) REVERT: K 213 GLU cc_start: 0.7391 (mp0) cc_final: 0.6861 (mp0) REVERT: K 224 LYS cc_start: 0.6192 (ttpp) cc_final: 0.5717 (pttp) REVERT: K 306 MET cc_start: 0.4414 (mmp) cc_final: 0.4110 (mmp) REVERT: K 400 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7155 (t-90) REVERT: K 403 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.6988 (ttp-110) REVERT: L 12 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.6947 (mtp180) REVERT: L 17 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7222 (tmt-80) REVERT: L 75 GLU cc_start: 0.8272 (tp30) cc_final: 0.7851 (tp30) REVERT: L 79 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8022 (ttpt) REVERT: L 193 GLN cc_start: 0.7557 (pt0) cc_final: 0.7271 (pt0) REVERT: L 224 LYS cc_start: 0.6143 (ttpp) cc_final: 0.5763 (pttp) REVERT: L 236 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5791 (mt) REVERT: L 283 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5835 (mpp80) REVERT: L 306 MET cc_start: 0.4611 (mmp) cc_final: 0.4204 (mmp) REVERT: L 400 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.7075 (t-90) REVERT: M 12 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.6812 (mtp180) REVERT: M 17 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7185 (tmt-80) REVERT: M 75 GLU cc_start: 0.8221 (tp30) cc_final: 0.7788 (tp30) REVERT: M 184 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: M 213 GLU cc_start: 0.7256 (mp0) cc_final: 0.6699 (mp0) REVERT: M 224 LYS cc_start: 0.6306 (ttpp) cc_final: 0.5888 (pttp) REVERT: M 264 ASN cc_start: 0.5892 (OUTLIER) cc_final: 0.5610 (t0) REVERT: M 306 MET cc_start: 0.4301 (mmp) cc_final: 0.4090 (mmp) REVERT: M 400 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7159 (t-90) REVERT: M 403 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.7174 (mtt-85) REVERT: M 483 GLU cc_start: 0.7827 (pt0) cc_final: 0.7377 (mt-10) REVERT: N 12 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7161 (mtp180) REVERT: N 17 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7219 (tmt-80) REVERT: N 75 GLU cc_start: 0.8280 (tp30) cc_final: 0.7748 (tp30) REVERT: N 79 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7824 (mtpt) REVERT: N 184 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: N 224 LYS cc_start: 0.6175 (ttpp) cc_final: 0.5728 (pttp) REVERT: N 320 LYS cc_start: 0.7299 (tptt) cc_final: 0.6965 (tppt) REVERT: N 321 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7136 (ttt-90) REVERT: N 400 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.7250 (t-90) REVERT: N 403 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.7064 (ttp-170) outliers start: 371 outliers final: 194 residues processed: 1133 average time/residue: 1.3088 time to fit residues: 1884.3183 Evaluate side-chains 1137 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 253 poor density : 884 time to evaluate : 4.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 47 THR 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 193 GLN 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 264 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 400 HIS Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 12 ARG 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 176 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 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 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 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 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 320 LYS Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 400 HIS Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 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 184 ASP 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 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 47 THR 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 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 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 331 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 400 HIS Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 12 ARG 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 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 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 321 ARG Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain 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 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 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 176 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 276 LYS Chi-restraints excluded: chain L residue 283 ARG Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 320 LYS Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 400 HIS Chi-restraints excluded: chain 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 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 320 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 263 optimal weight: 5.9990 chunk 522 optimal weight: 4.9990 chunk 707 optimal weight: 7.9990 chunk 482 optimal weight: 3.9990 chunk 499 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 462 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 427 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 C 36 ASN C 365 GLN D 365 GLN E 365 GLN F 365 GLN G 318 GLN G 365 GLN H 36 ASN H 365 GLN J 365 GLN K 365 GLN L 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.205332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124161 restraints weight = 55071.787| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.71 r_work: 0.3254 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 56042 Z= 0.305 Angle : 0.596 9.531 75712 Z= 0.308 Chirality : 0.044 0.161 9142 Planarity : 0.004 0.033 9884 Dihedral : 4.646 46.660 7936 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.81 % Favored : 97.00 % Rotamer: Outliers : 6.40 % Allowed : 22.91 % Favored : 70.69 % 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: 1.29 (0.10), residues: 7462 helix: 1.99 (0.08), residues: 4228 sheet: -0.46 (0.17), residues: 966 loop : -0.69 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 23 HIS 0.004 0.002 HIS K 400 PHE 0.007 0.001 PHE U 25 TYR 0.014 0.001 TYR C 505 ARG 0.006 0.000 ARG D 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14924 Ramachandran restraints generated. 7462 Oldfield, 0 Emsley, 7462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 373 poor density : 889 time to evaluate : 4.555 Fit side-chains REVERT: A 17 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7211 (tmt-80) REVERT: A 75 GLU cc_start: 0.8250 (tp30) cc_final: 0.7823 (tp30) REVERT: A 79 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8027 (ttpt) REVERT: A 184 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: A 193 GLN cc_start: 0.7653 (pt0) cc_final: 0.7414 (pt0) REVERT: A 213 GLU cc_start: 0.7382 (mp0) cc_final: 0.6833 (mp0) REVERT: A 224 LYS cc_start: 0.6208 (ttpp) cc_final: 0.5776 (pttp) REVERT: A 306 MET cc_start: 0.4455 (mmp) cc_final: 0.4061 (mmp) REVERT: A 400 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.7020 (t-90) REVERT: A 403 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6984 (ttp-170) REVERT: A 483 GLU cc_start: 0.7872 (pt0) cc_final: 0.7492 (mt-10) REVERT: B 17 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7193 (tmt-80) REVERT: B 75 GLU cc_start: 0.8225 (tp30) cc_final: 0.7831 (tp30) REVERT: B 184 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: B 224 LYS cc_start: 0.6226 (ttpp) cc_final: 0.5778 (pttp) REVERT: B 306 MET cc_start: 0.4280 (mmp) cc_final: 0.3889 (mmp) REVERT: B 366 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: B 400 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7067 (t-90) REVERT: B 403 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7054 (ttp-170) REVERT: C 12 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6926 (mtp180) REVERT: C 17 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7231 (tmt-80) REVERT: C 75 GLU cc_start: 0.8231 (tp30) cc_final: 0.7865 (tp30) REVERT: C 79 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7965 (ttpt) REVERT: C 165 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.7006 (mtt) REVERT: C 184 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6833 (m-30) REVERT: C 193 GLN cc_start: 0.7683 (pt0) cc_final: 0.7397 (pt0) REVERT: C 224 LYS cc_start: 0.6280 (ttpp) cc_final: 0.5771 (pttp) REVERT: C 236 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5860 (mt) REVERT: C 283 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6053 (mpp80) REVERT: C 306 MET cc_start: 0.4471 (mmp) cc_final: 0.4093 (mmp) REVERT: D 12 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.6868 (mtp180) REVERT: D 17 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7187 (tmt-80) REVERT: D 75 GLU cc_start: 0.8223 (tp30) cc_final: 0.7813 (tp30) REVERT: D 184 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: D 193 GLN cc_start: 0.7596 (pt0) cc_final: 0.7264 (pt0) REVERT: D 213 GLU cc_start: 0.7414 (mp0) cc_final: 0.6907 (mp0) REVERT: D 224 LYS cc_start: 0.6243 (ttpp) cc_final: 0.5736 (pttp) REVERT: D 306 MET cc_start: 0.4247 (mmp) cc_final: 0.3855 (mmp) REVERT: D 400 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7160 (t-90) REVERT: D 403 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.6986 (ttp-110) REVERT: E 12 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6955 (mtp180) REVERT: E 17 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7233 (tmt-80) REVERT: E 43 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6998 (p90) REVERT: E 75 GLU cc_start: 0.8289 (tp30) cc_final: 0.7849 (tp30) REVERT: E 193 GLN cc_start: 0.7533 (pt0) cc_final: 0.7218 (pt0) REVERT: E 224 LYS cc_start: 0.6122 (ttpp) cc_final: 0.5683 (pttp) REVERT: E 236 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5809 (mt) REVERT: E 283 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6047 (mpp80) REVERT: E 306 MET cc_start: 0.4329 (mmp) cc_final: 0.4058 (mmp) REVERT: E 400 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.6997 (t-90) REVERT: F 12 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6821 (mtp180) REVERT: F 17 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7218 (tmt-80) REVERT: F 75 GLU cc_start: 0.8250 (tp30) cc_final: 0.7824 (tp30) REVERT: F 224 LYS cc_start: 0.6346 (ttpp) cc_final: 0.5911 (pttp) REVERT: F 264 ASN cc_start: 0.5887 (OUTLIER) cc_final: 0.5614 (t0) REVERT: F 306 MET cc_start: 0.4501 (mmp) cc_final: 0.4037 (mmp) REVERT: F 400 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7112 (t-90) REVERT: F 403 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.6954 (ttp-170) REVERT: G 12 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7064 (mtp180) REVERT: G 17 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7233 (tmt-80) REVERT: G 75 GLU cc_start: 0.8284 (tp30) cc_final: 0.7758 (tp30) REVERT: G 79 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7806 (mtpt) REVERT: G 184 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6891 (m-30) REVERT: G 224 LYS cc_start: 0.6236 (ttpp) cc_final: 0.5649 (pttp) REVERT: G 306 MET cc_start: 0.4003 (mmp) cc_final: 0.3795 (mmp) REVERT: G 400 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7201 (t-90) REVERT: G 403 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7011 (ttp-170) REVERT: H 17 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7213 (tmt-80) REVERT: H 75 GLU cc_start: 0.8243 (tp30) cc_final: 0.7817 (tp30) REVERT: H 79 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (ttpt) REVERT: H 184 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: H 193 GLN cc_start: 0.7643 (pt0) cc_final: 0.7391 (pt0) REVERT: H 213 GLU cc_start: 0.7397 (mp0) cc_final: 0.6885 (mp0) REVERT: H 224 LYS cc_start: 0.6204 (ttpp) cc_final: 0.5768 (pttp) REVERT: H 306 MET cc_start: 0.4453 (mmp) cc_final: 0.4060 (mmp) REVERT: H 400 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7021 (t-90) REVERT: H 403 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.6980 (ttp-170) REVERT: H 483 GLU cc_start: 0.7861 (pt0) cc_final: 0.7486 (mt-10) REVERT: I 12 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.6810 (mtp180) REVERT: I 17 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7191 (tmt-80) REVERT: I 75 GLU cc_start: 0.8234 (tp30) cc_final: 0.7836 (tp30) REVERT: I 184 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: I 224 LYS cc_start: 0.6225 (ttpp) cc_final: 0.5781 (pttp) REVERT: I 306 MET cc_start: 0.4235 (mmp) cc_final: 0.3851 (mmp) REVERT: I 366 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: I 400 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: I 403 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.7061 (ttp-170) REVERT: J 12 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.6930 (mtp180) REVERT: J 17 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7229 (tmt-80) REVERT: J 75 GLU cc_start: 0.8244 (tp30) cc_final: 0.7878 (tp30) REVERT: J 79 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7975 (ttpt) REVERT: J 165 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6985 (mtt) REVERT: J 184 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: J 193 GLN cc_start: 0.7722 (pt0) cc_final: 0.7417 (pt0) REVERT: J 224 LYS cc_start: 0.6258 (ttpp) cc_final: 0.5743 (pttp) REVERT: J 236 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5862 (mt) REVERT: J 283 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6070 (mpp80) REVERT: J 306 MET cc_start: 0.4326 (mmp) cc_final: 0.3958 (mmp) REVERT: J 321 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6524 (ttt-90) REVERT: K 12 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.6873 (mtp180) REVERT: K 17 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7182 (tmt-80) REVERT: K 75 GLU cc_start: 0.8224 (tp30) cc_final: 0.7816 (tp30) REVERT: K 184 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: K 193 GLN cc_start: 0.7596 (pt0) cc_final: 0.7269 (pt0) REVERT: K 213 GLU cc_start: 0.7410 (mp0) cc_final: 0.6907 (mp0) REVERT: K 224 LYS cc_start: 0.6257 (ttpp) cc_final: 0.5739 (pttp) REVERT: K 306 MET cc_start: 0.4466 (mmp) cc_final: 0.4055 (mmp) REVERT: K 400 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7149 (t-90) REVERT: K 403 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.6979 (ttp-110) REVERT: L 12 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6955 (mtp180) REVERT: L 17 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7229 (tmt-80) REVERT: L 43 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6985 (p90) REVERT: L 75 GLU cc_start: 0.8281 (tp30) cc_final: 0.7847 (tp30) REVERT: L 193 GLN cc_start: 0.7542 (pt0) cc_final: 0.7264 (pt0) REVERT: L 224 LYS cc_start: 0.6117 (ttpp) cc_final: 0.5754 (pttp) REVERT: L 236 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5791 (mt) REVERT: L 283 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6029 (mpp80) REVERT: L 306 MET cc_start: 0.4362 (mmp) cc_final: 0.4038 (mmp) REVERT: L 400 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.6993 (t-90) REVERT: M 12 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.6817 (mtp180) REVERT: M 17 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7219 (tmt-80) REVERT: M 75 GLU cc_start: 0.8251 (tp30) cc_final: 0.7825 (tp30) REVERT: M 213 GLU cc_start: 0.7260 (mp0) cc_final: 0.6725 (mp0) REVERT: M 224 LYS cc_start: 0.6307 (ttpp) cc_final: 0.5859 (pttp) REVERT: M 264 ASN cc_start: 0.5894 (OUTLIER) cc_final: 0.5618 (t0) REVERT: M 306 MET cc_start: 0.4343 (mmp) cc_final: 0.3977 (mmp) REVERT: M 400 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7134 (t-90) REVERT: M 403 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.6948 (ttp-170) REVERT: M 483 GLU cc_start: 0.7831 (pt0) cc_final: 0.7405 (mt-10) REVERT: N 12 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7047 (mtp180) REVERT: N 17 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7224 (tmt-80) REVERT: N 75 GLU cc_start: 0.8285 (tp30) cc_final: 0.7764 (tp30) REVERT: N 79 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7811 (mtpt) REVERT: N 184 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6876 (m-30) REVERT: N 224 LYS cc_start: 0.6162 (ttpp) cc_final: 0.5642 (pttp) REVERT: N 306 MET cc_start: 0.3946 (mmp) cc_final: 0.3724 (mmp) REVERT: N 321 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7213 (ttt-90) REVERT: N 400 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7203 (t-90) REVERT: N 403 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7020 (ttp-170) outliers start: 373 outliers final: 206 residues processed: 1129 average time/residue: 1.3239 time to fit residues: 1896.6227 Evaluate side-chains 1135 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 873 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 47 THR 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 47 THR 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 331 ILE 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 419 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 12 ARG 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 176 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 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 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 ASP 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 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 47 THR Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET 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 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 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 184 ASP 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 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 47 THR 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 47 THR 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 331 ILE 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 12 ARG 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 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 283 ARG Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 321 ARG Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain 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 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 419 ILE 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 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 47 THR Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 MET 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 176 VAL Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 276 LYS Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 741 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 337 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 519 optimal weight: 1.9990 chunk 661 optimal weight: 20.0000 chunk 522 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 chunk 341 optimal weight: 0.9980 chunk 321 optimal weight: 0.9990 chunk 362 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN B 36 ASN C 365 GLN D 365 GLN E 365 GLN F 36 ASN F 365 GLN G 36 ASN G 365 GLN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.206413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125842 restraints weight = 55018.838| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.70 r_work: 0.3272 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 56042 Z= 0.233 Angle : 0.565 9.748 75712 Z= 0.293 Chirality : 0.043 0.179 9142 Planarity : 0.003 0.032 9884 Dihedral : 4.541 56.473 7936 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.68 % Favored : 97.13 % Rotamer: Outliers : 5.27 % Allowed : 24.16 % Favored : 70.57 % 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: 1.38 (0.10), residues: 7462 helix: 2.09 (0.08), residues: 4228 sheet: -0.45 (0.18), residues: 966 loop : -0.70 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 23 HIS 0.003 0.001 HIS L 400 PHE 0.007 0.001 PHE G 194 TYR 0.011 0.001 TYR C 505 ARG 0.006 0.000 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 1203 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 307 poor density : 896 time to evaluate : 4.753 Fit side-chains REVERT: A 17 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7212 (tmt-80) REVERT: A 75 GLU cc_start: 0.8233 (tp30) cc_final: 0.7804 (tp30) REVERT: A 79 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8006 (ttpt) REVERT: A 193 GLN cc_start: 0.7577 (pt0) cc_final: 0.7328 (pt0) REVERT: A 224 LYS cc_start: 0.6210 (ttpp) cc_final: 0.5782 (pttp) REVERT: A 306 MET cc_start: 0.4524 (mmp) cc_final: 0.4283 (mmp) REVERT: A 321 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6151 (ttt-90) REVERT: A 400 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7000 (t-90) REVERT: A 403 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.6976 (ttp-170) REVERT: A 483 GLU cc_start: 0.7862 (pt0) cc_final: 0.7475 (mt-10) REVERT: B 17 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7176 (tmt-80) REVERT: B 75 GLU cc_start: 0.8209 (tp30) cc_final: 0.7805 (tp30) REVERT: B 224 LYS cc_start: 0.6171 (ttpp) cc_final: 0.5679 (pttp) REVERT: B 306 MET cc_start: 0.4290 (mmp) cc_final: 0.3974 (mmp) REVERT: B 403 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7054 (ttp-170) REVERT: C 12 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6895 (mtp180) REVERT: C 17 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7205 (tmt-80) REVERT: C 75 GLU cc_start: 0.8227 (tp30) cc_final: 0.7923 (tp30) REVERT: C 79 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7958 (ttpt) REVERT: C 165 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6979 (mtt) REVERT: C 184 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6825 (m-30) REVERT: C 224 LYS cc_start: 0.6278 (ttpp) cc_final: 0.5797 (pttp) REVERT: C 236 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5809 (mt) REVERT: C 283 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6046 (mpp80) REVERT: C 306 MET cc_start: 0.4401 (mmp) cc_final: 0.4034 (mmp) REVERT: D 12 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.6860 (mtp180) REVERT: D 17 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7183 (tmt-80) REVERT: D 75 GLU cc_start: 0.8196 (tp30) cc_final: 0.7792 (tp30) REVERT: D 193 GLN cc_start: 0.7557 (pt0) cc_final: 0.7245 (pt0) REVERT: D 213 GLU cc_start: 0.7462 (mp0) cc_final: 0.6950 (mp0) REVERT: D 224 LYS cc_start: 0.6239 (ttpp) cc_final: 0.5735 (pttp) REVERT: D 306 MET cc_start: 0.4168 (mmp) cc_final: 0.3803 (mmp) REVERT: D 400 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7198 (t-90) REVERT: D 403 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.6964 (ttp-110) REVERT: E 12 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.6929 (mtp180) REVERT: E 17 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.7218 (tmt-80) REVERT: E 75 GLU cc_start: 0.8271 (tp30) cc_final: 0.7894 (tp30) REVERT: E 224 LYS cc_start: 0.6142 (ttpp) cc_final: 0.5768 (pttp) REVERT: E 283 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.5987 (mpp80) REVERT: E 306 MET cc_start: 0.4387 (mmp) cc_final: 0.4137 (mmp) REVERT: E 400 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7025 (t-90) REVERT: F 12 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.6838 (mtp180) REVERT: F 17 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7190 (tmt-80) REVERT: F 75 GLU cc_start: 0.8197 (tp30) cc_final: 0.7713 (tp30) REVERT: F 224 LYS cc_start: 0.6301 (ttpp) cc_final: 0.5846 (pttp) REVERT: F 264 ASN cc_start: 0.5861 (OUTLIER) cc_final: 0.5581 (t0) REVERT: F 306 MET cc_start: 0.4515 (mmp) cc_final: 0.4213 (mmp) REVERT: F 400 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7118 (t-90) REVERT: F 403 ARG cc_start: 0.7432 (ttm-80) cc_final: 0.6957 (ttp-170) REVERT: G 12 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7129 (mtp180) REVERT: G 17 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7224 (tmt-80) REVERT: G 75 GLU cc_start: 0.8285 (tp30) cc_final: 0.7740 (tp30) REVERT: G 79 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7802 (mtpt) REVERT: G 224 LYS cc_start: 0.6147 (ttpp) cc_final: 0.5735 (pttp) REVERT: G 306 MET cc_start: 0.4098 (mmp) cc_final: 0.3807 (mmp) REVERT: G 321 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.7094 (ttt-90) REVERT: G 388 MET cc_start: 0.5948 (tpt) cc_final: 0.5733 (tpp) REVERT: G 400 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.7232 (t-90) REVERT: G 403 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7072 (ttp-170) REVERT: H 17 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7208 (tmt-80) REVERT: H 75 GLU cc_start: 0.8215 (tp30) cc_final: 0.7785 (tp30) REVERT: H 79 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7991 (ttpt) REVERT: H 193 GLN cc_start: 0.7602 (pt0) cc_final: 0.7354 (pt0) REVERT: H 213 GLU cc_start: 0.7419 (mp0) cc_final: 0.6919 (mp0) REVERT: H 224 LYS cc_start: 0.6198 (ttpp) cc_final: 0.5767 (pttp) REVERT: H 306 MET cc_start: 0.4513 (mmp) cc_final: 0.4272 (mmp) REVERT: H 400 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7012 (t-90) REVERT: H 403 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.6970 (ttp-170) REVERT: H 483 GLU cc_start: 0.7859 (pt0) cc_final: 0.7470 (mt-10) REVERT: I 12 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.6795 (mtp180) REVERT: I 17 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7168 (tmt-80) REVERT: I 75 GLU cc_start: 0.8217 (tp30) cc_final: 0.7803 (tp30) REVERT: I 224 LYS cc_start: 0.6168 (ttpp) cc_final: 0.5676 (pttp) REVERT: I 306 MET cc_start: 0.4266 (mmp) cc_final: 0.3951 (mmp) REVERT: I 403 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.7053 (ttp-170) REVERT: J 12 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6895 (mtp180) REVERT: J 17 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7204 (tmt-80) REVERT: J 75 GLU cc_start: 0.8227 (tp30) cc_final: 0.7925 (tp30) REVERT: J 79 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: J 165 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6954 (mtt) REVERT: J 184 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6842 (m-30) REVERT: J 193 GLN cc_start: 0.7660 (pt0) cc_final: 0.7391 (pt0) REVERT: J 224 LYS cc_start: 0.6284 (ttpp) cc_final: 0.5808 (pttp) REVERT: J 283 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6047 (mpp80) REVERT: J 306 MET cc_start: 0.4296 (mmp) cc_final: 0.3930 (mmp) REVERT: J 321 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6704 (ttt-90) REVERT: K 12 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.6862 (mtp180) REVERT: K 17 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7176 (tmt-80) REVERT: K 75 GLU cc_start: 0.8199 (tp30) cc_final: 0.7797 (tp30) REVERT: K 193 GLN cc_start: 0.7554 (pt0) cc_final: 0.7249 (pt0) REVERT: K 213 GLU cc_start: 0.7462 (mp0) cc_final: 0.6947 (mp0) REVERT: K 224 LYS cc_start: 0.6231 (ttpp) cc_final: 0.5728 (pttp) REVERT: K 306 MET cc_start: 0.4263 (mmp) cc_final: 0.3863 (mmp) REVERT: K 400 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7185 (t-90) REVERT: K 403 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6948 (ttp-110) REVERT: L 12 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.6924 (mtp180) REVERT: L 17 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7222 (tmt-80) REVERT: L 75 GLU cc_start: 0.8266 (tp30) cc_final: 0.7890 (tp30) REVERT: L 193 GLN cc_start: 0.7495 (pt0) cc_final: 0.7221 (pt0) REVERT: L 224 LYS cc_start: 0.6194 (ttpp) cc_final: 0.5831 (pttp) REVERT: L 283 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.5980 (mpp80) REVERT: L 306 MET cc_start: 0.4441 (mmp) cc_final: 0.4189 (mmp) REVERT: L 400 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7020 (t-90) REVERT: M 12 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6821 (mtp180) REVERT: M 17 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7185 (tmt-80) REVERT: M 75 GLU cc_start: 0.8204 (tp30) cc_final: 0.7716 (tp30) REVERT: M 213 GLU cc_start: 0.7294 (mp0) cc_final: 0.6772 (mp0) REVERT: M 224 LYS cc_start: 0.6297 (ttpp) cc_final: 0.5823 (pttp) REVERT: M 264 ASN cc_start: 0.5874 (OUTLIER) cc_final: 0.5590 (t0) REVERT: M 294 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6759 (tp) REVERT: M 306 MET cc_start: 0.4310 (mmp) cc_final: 0.3978 (mmp) REVERT: M 400 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7133 (t-90) REVERT: M 403 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.6958 (ttp-170) REVERT: M 483 GLU cc_start: 0.7808 (pt0) cc_final: 0.7372 (mt-10) REVERT: N 12 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7134 (mtp180) REVERT: N 17 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7218 (tmt-80) REVERT: N 75 GLU cc_start: 0.8278 (tp30) cc_final: 0.7737 (tp30) REVERT: N 79 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7798 (mtpt) REVERT: N 224 LYS cc_start: 0.6143 (ttpp) cc_final: 0.5682 (pttp) REVERT: N 306 MET cc_start: 0.4015 (mmp) cc_final: 0.3717 (mmp) REVERT: N 400 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7229 (t-90) REVERT: N 403 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7074 (ttp-170) outliers start: 307 outliers final: 197 residues processed: 1110 average time/residue: 1.3259 time to fit residues: 1870.5773 Evaluate side-chains 1119 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 881 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 MET Chi-restraints excluded: chain A residue 47 THR 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 321 ARG 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 47 THR 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 329 THR 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 12 ARG Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 47 THR 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 176 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 209 THR 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 47 THR Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 47 THR 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 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 MET 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 331 ILE 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 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 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 47 THR Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 400 HIS Chi-restraints excluded: chain H residue 419 ILE Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 47 THR 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 331 ILE Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 12 ARG Chi-restraints excluded: chain J residue 47 THR 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 176 VAL Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 264 ASN Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 283 ARG Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 321 ARG Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain 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 47 THR Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 419 ILE Chi-restraints excluded: chain L residue 12 ARG Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 153 SER Chi-restraints excluded: chain L residue 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 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 294 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 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 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 705 optimal weight: 10.0000 chunk 507 optimal weight: 5.9990 chunk 250 optimal weight: 0.2980 chunk 608 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 412 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 L 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.204259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123079 restraints weight = 54916.093| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.69 r_work: 0.3238 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 56042 Z= 0.377 Angle : 0.643 10.225 75712 Z= 0.333 Chirality : 0.046 0.191 9142 Planarity : 0.004 0.034 9884 Dihedral : 4.734 58.229 7936 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.99 % Favored : 96.82 % Rotamer: Outliers : 5.34 % Allowed : 23.94 % Favored : 70.72 % 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: 1.02 (0.09), residues: 7462 helix: 1.80 (0.08), residues: 4242 sheet: -0.59 (0.17), residues: 966 loop : -0.87 (0.11), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 23 HIS 0.007 0.003 HIS L 400 PHE 0.007 0.002 PHE U 25 TYR 0.015 0.001 TYR C 505 ARG 0.005 0.001 ARG J 12 *********************** 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 1180 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 311 poor density : 869 time to evaluate : 4.553 Fit side-chains REVERT: A 17 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7244 (tmt-80) REVERT: A 75 GLU cc_start: 0.8267 (tp30) cc_final: 0.7940 (tp30) REVERT: A 193 GLN cc_start: 0.7576 (pt0) cc_final: 0.7284 (pt0) REVERT: A 224 LYS cc_start: 0.6297 (ttpp) cc_final: 0.5821 (pttp) REVERT: A 306 MET cc_start: 0.4471 (mmp) cc_final: 0.4083 (mmp) REVERT: A 403 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7015 (ttp-170) REVERT: A 483 GLU cc_start: 0.7866 (pt0) cc_final: 0.7490 (mt-10) REVERT: B 17 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7189 (tmt-80) REVERT: B 75 GLU cc_start: 0.8271 (tp30) cc_final: 0.7864 (tp30) REVERT: B 224 LYS cc_start: 0.6199 (ttpp) cc_final: 0.5666 (pttp) REVERT: B 306 MET cc_start: 0.4261 (mmp) cc_final: 0.3946 (mmp) REVERT: B 366 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: B 403 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7037 (ttp-110) REVERT: C 12 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6944 (mtp180) REVERT: C 17 ARG cc_start: 0.8177 (ttp-110) cc_final: 0.7227 (tmt-80) REVERT: C 75 GLU cc_start: 0.8266 (tp30) cc_final: 0.7914 (tp30) REVERT: C 79 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7888 (mtmm) REVERT: C 165 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.7006 (mtt) REVERT: C 184 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6876 (m-30) REVERT: C 224 LYS cc_start: 0.6239 (ttpp) cc_final: 0.5758 (pttp) REVERT: C 283 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6035 (mpp80) REVERT: C 306 MET cc_start: 0.4218 (mmp) cc_final: 0.3845 (mmp) REVERT: D 12 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.6874 (mtp180) REVERT: D 17 ARG cc_start: 0.8171 (ttp-110) cc_final: 0.7209 (tmt-80) REVERT: D 75 GLU cc_start: 0.8257 (tp30) cc_final: 0.7853 (tp30) REVERT: D 193 GLN cc_start: 0.7575 (pt0) cc_final: 0.7260 (pt0) REVERT: D 213 GLU cc_start: 0.7442 (mp0) cc_final: 0.6896 (mp0) REVERT: D 224 LYS cc_start: 0.6281 (ttpp) cc_final: 0.5727 (pttp) REVERT: D 306 MET cc_start: 0.4197 (mmp) cc_final: 0.3983 (mmp) REVERT: D 403 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.6994 (ttp-110) REVERT: E 12 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.6986 (mtp180) REVERT: E 17 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7247 (tmt-80) REVERT: E 75 GLU cc_start: 0.8295 (tp30) cc_final: 0.7856 (tp30) REVERT: E 224 LYS cc_start: 0.6140 (ttpp) cc_final: 0.5669 (pttp) REVERT: E 283 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5917 (mpp80) REVERT: E 306 MET cc_start: 0.4256 (mmp) cc_final: 0.3944 (mmp) REVERT: F 12 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.6864 (mtp180) REVERT: F 17 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7221 (tmt-80) REVERT: F 43 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6981 (p90) REVERT: F 75 GLU cc_start: 0.8268 (tp30) cc_final: 0.7830 (tp30) REVERT: F 79 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8038 (mtpt) REVERT: F 224 LYS cc_start: 0.6265 (ttpp) cc_final: 0.5857 (pttp) REVERT: F 264 ASN cc_start: 0.5814 (OUTLIER) cc_final: 0.5539 (t0) REVERT: F 306 MET cc_start: 0.4408 (mmp) cc_final: 0.4085 (mmp) REVERT: F 403 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7012 (ttp-170) REVERT: G 12 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7090 (mtp180) REVERT: G 17 ARG cc_start: 0.8205 (ttp-110) cc_final: 0.7239 (tmt-80) REVERT: G 75 GLU cc_start: 0.8320 (tp30) cc_final: 0.7815 (tp30) REVERT: G 79 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7830 (mtpt) REVERT: G 224 LYS cc_start: 0.6114 (ttpp) cc_final: 0.5611 (pttp) REVERT: G 306 MET cc_start: 0.4133 (mmp) cc_final: 0.3795 (mmp) REVERT: G 400 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7146 (t-90) REVERT: G 403 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7021 (ttp-170) REVERT: H 17 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7249 (tmt-80) REVERT: H 75 GLU cc_start: 0.8258 (tp30) cc_final: 0.7930 (tp30) REVERT: H 193 GLN cc_start: 0.7586 (pt0) cc_final: 0.7290 (pt0) REVERT: H 224 LYS cc_start: 0.6255 (ttpp) cc_final: 0.5773 (pttp) REVERT: H 306 MET cc_start: 0.4451 (mmp) cc_final: 0.4071 (mmp) REVERT: H 403 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7000 (ttp-170) REVERT: H 483 GLU cc_start: 0.7862 (pt0) cc_final: 0.7487 (mt-10) REVERT: I 12 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.6864 (mtp180) REVERT: I 17 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7186 (tmt-80) REVERT: I 75 GLU cc_start: 0.8268 (tp30) cc_final: 0.7862 (tp30) REVERT: I 224 LYS cc_start: 0.6199 (ttpp) cc_final: 0.5665 (pttp) REVERT: I 306 MET cc_start: 0.4239 (mmp) cc_final: 0.3925 (mmp) REVERT: I 403 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7030 (ttp-110) REVERT: J 12 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.6947 (mtp180) REVERT: J 17 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7231 (tmt-80) REVERT: J 75 GLU cc_start: 0.8270 (tp30) cc_final: 0.7918 (tp30) REVERT: J 79 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7887 (mtmm) REVERT: J 165 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6990 (mtt) REVERT: J 184 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: J 193 GLN cc_start: 0.7655 (pt0) cc_final: 0.7369 (pt0) REVERT: J 224 LYS cc_start: 0.6225 (ttpp) cc_final: 0.5741 (pttp) REVERT: J 283 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6023 (mpp80) REVERT: J 306 MET cc_start: 0.4235 (mmp) cc_final: 0.3854 (mmp) REVERT: J 321 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6535 (ttt-90) REVERT: K 12 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.6872 (mtp180) REVERT: K 17 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7186 (tmt-80) REVERT: K 75 GLU cc_start: 0.8244 (tp30) cc_final: 0.7837 (tp30) REVERT: K 213 GLU cc_start: 0.7441 (mp0) cc_final: 0.6935 (mp0) REVERT: K 224 LYS cc_start: 0.6286 (ttpp) cc_final: 0.5731 (pttp) REVERT: K 306 MET cc_start: 0.4246 (mmp) cc_final: 0.4034 (mmp) REVERT: K 403 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.7016 (ttp-170) REVERT: L 12 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.6983 (mtp180) REVERT: L 17 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7258 (tmt-80) REVERT: L 75 GLU cc_start: 0.8293 (tp30) cc_final: 0.7855 (tp30) REVERT: L 193 GLN cc_start: 0.7421 (pt0) cc_final: 0.7211 (pt0) REVERT: L 224 LYS cc_start: 0.6138 (ttpp) cc_final: 0.5615 (pttp) REVERT: L 283 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5905 (mpp80) REVERT: L 306 MET cc_start: 0.4317 (mmp) cc_final: 0.3987 (mmp) REVERT: M 12 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.6851 (mtp180) REVERT: M 17 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7223 (tmt-80) REVERT: M 75 GLU cc_start: 0.8283 (tp30) cc_final: 0.7839 (tp30) REVERT: M 79 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8030 (mtpt) REVERT: M 224 LYS cc_start: 0.6256 (ttpp) cc_final: 0.5843 (pttp) REVERT: M 264 ASN cc_start: 0.5813 (OUTLIER) cc_final: 0.5541 (t0) REVERT: M 294 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6715 (tp) REVERT: M 306 MET cc_start: 0.4319 (mmp) cc_final: 0.3897 (mmp) REVERT: M 403 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7005 (ttp-170) REVERT: M 483 GLU cc_start: 0.7860 (pt0) cc_final: 0.7425 (mt-10) REVERT: N 12 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7075 (mtp180) REVERT: N 17 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7236 (tmt-80) REVERT: N 75 GLU cc_start: 0.8321 (tp30) cc_final: 0.7816 (tp30) REVERT: N 79 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7833 (mtpt) REVERT: N 184 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: N 224 LYS cc_start: 0.6136 (ttpp) cc_final: 0.5609 (pttp) REVERT: N 306 MET cc_start: 0.3969 (mmp) cc_final: 0.3589 (mmp) REVERT: N 400 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7146 (t-90) REVERT: N 403 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7030 (ttp-170) outliers start: 311 outliers final: 196 residues processed: 1081 average time/residue: 1.3602 time to fit residues: 1857.8717 Evaluate side-chains 1089 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 859 time to evaluate : 4.564 ------------------------------------------------------------------------------- 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 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 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 419 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 12 ARG 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 176 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 209 THR 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 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 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 247 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 400 HIS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 43 PHE 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 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 47 THR 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 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 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL 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 400 HIS Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 522 ASP Chi-restraints excluded: chain J residue 12 ARG 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 176 VAL Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 209 THR 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 321 ARG Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 386 VAL Chi-restraints excluded: chain J residue 400 HIS Chi-restraints excluded: chain 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 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 176 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 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 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 294 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 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 153 SER Chi-restraints excluded: chain N residue 168 VAL Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 284 optimal weight: 10.0000 chunk 187 optimal weight: 0.0980 chunk 165 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 491 optimal weight: 7.9990 chunk 333 optimal weight: 20.0000 chunk 729 optimal weight: 20.0000 chunk 158 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 653 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 36 ASN D 365 GLN E 36 ASN E 365 GLN F 365 GLN G 365 GLN H 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127947 restraints weight = 54980.426| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.70 r_work: 0.3299 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 56042 Z= 0.177 Angle : 0.545 10.597 75712 Z= 0.286 Chirality : 0.042 0.162 9142 Planarity : 0.003 0.033 9884 Dihedral : 4.407 54.950 7936 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.53 % Favored : 97.28 % Rotamer: Outliers : 3.83 % Allowed : 25.58 % Favored : 70.59 % 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: 1.41 (0.10), residues: 7462 helix: 2.10 (0.08), residues: 4242 sheet: -1.00 (0.18), residues: 826 loop : -0.43 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 1 18 HIS 0.001 0.001 HIS A 400 PHE 0.006 0.001 PHE F 65 TYR 0.011 0.001 TYR C 505 ARG 0.005 0.000 ARG D 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 1118 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 895 time to evaluate : 4.642 Fit side-chains REVERT: A 17 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7198 (tmt-80) REVERT: A 75 GLU cc_start: 0.8192 (tp30) cc_final: 0.7754 (tp30) REVERT: A 79 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7934 (ttpt) REVERT: A 193 GLN cc_start: 0.7561 (pt0) cc_final: 0.7309 (pt0) REVERT: A 224 LYS cc_start: 0.6238 (ttpp) cc_final: 0.5855 (pttp) REVERT: A 288 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6725 (mp) REVERT: A 403 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.6991 (ttp-170) REVERT: A 444 ARG cc_start: 0.8468 (ttm110) cc_final: 0.7469 (tpt90) REVERT: A 483 GLU cc_start: 0.7831 (pt0) cc_final: 0.7458 (mt-10) REVERT: B 17 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7180 (tmt-80) REVERT: B 75 GLU cc_start: 0.8159 (tp30) cc_final: 0.7755 (tp30) REVERT: B 224 LYS cc_start: 0.6232 (ttpp) cc_final: 0.5709 (pttp) REVERT: B 306 MET cc_start: 0.4142 (mmp) cc_final: 0.3935 (mmp) REVERT: B 403 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7016 (ttp-170) REVERT: C 17 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.7169 (tmt-80) REVERT: C 75 GLU cc_start: 0.8208 (tp30) cc_final: 0.7907 (tp30) REVERT: C 79 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7958 (ttpt) REVERT: C 165 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6916 (mtt) REVERT: C 224 LYS cc_start: 0.6290 (ttpp) cc_final: 0.5823 (pttp) REVERT: C 283 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6021 (mpp80) REVERT: C 306 MET cc_start: 0.4290 (mmp) cc_final: 0.4076 (mmp) REVERT: D 12 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.6828 (mtp180) REVERT: D 17 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7172 (tmt-80) REVERT: D 75 GLU cc_start: 0.8181 (tp30) cc_final: 0.7769 (tp30) REVERT: D 193 GLN cc_start: 0.7523 (pt0) cc_final: 0.7241 (pt0) REVERT: D 213 GLU cc_start: 0.7440 (mp0) cc_final: 0.6934 (mp0) REVERT: D 224 LYS cc_start: 0.6339 (ttpp) cc_final: 0.5956 (pttp) REVERT: D 306 MET cc_start: 0.4230 (mmp) cc_final: 0.3982 (mmp) REVERT: D 400 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7059 (t-90) REVERT: D 403 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.6960 (ttp-110) REVERT: E 12 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6933 (mtp180) REVERT: E 17 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7207 (tmt-80) REVERT: E 75 GLU cc_start: 0.8241 (tp30) cc_final: 0.7864 (tp30) REVERT: E 224 LYS cc_start: 0.6183 (ttpp) cc_final: 0.5770 (pttp) REVERT: E 283 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6008 (mpp80) REVERT: E 400 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: F 17 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7171 (tmt-80) REVERT: F 75 GLU cc_start: 0.8149 (tp30) cc_final: 0.7668 (tp30) REVERT: F 224 LYS cc_start: 0.6342 (ttpp) cc_final: 0.5890 (pttp) REVERT: F 264 ASN cc_start: 0.5809 (OUTLIER) cc_final: 0.5516 (t0) REVERT: F 306 MET cc_start: 0.4539 (mmp) cc_final: 0.4335 (mmp) REVERT: F 400 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.7081 (t-90) REVERT: F 403 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.6986 (ttp-170) REVERT: F 444 ARG cc_start: 0.8497 (ttm110) cc_final: 0.7296 (tpt90) REVERT: G 17 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7216 (tmt-80) REVERT: G 75 GLU cc_start: 0.8257 (tp30) cc_final: 0.7721 (tp30) REVERT: G 79 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7784 (mtpt) REVERT: G 224 LYS cc_start: 0.6137 (ttpp) cc_final: 0.5714 (pttp) REVERT: G 400 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7182 (t-90) REVERT: G 403 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7070 (ttp-170) REVERT: H 17 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7199 (tmt-80) REVERT: H 75 GLU cc_start: 0.8179 (tp30) cc_final: 0.7740 (tp30) REVERT: H 79 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7924 (ttpt) REVERT: H 193 GLN cc_start: 0.7594 (pt0) cc_final: 0.7340 (pt0) REVERT: H 224 LYS cc_start: 0.6237 (ttpp) cc_final: 0.5852 (pttp) REVERT: H 288 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6725 (mp) REVERT: H 403 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.6993 (ttp-170) REVERT: H 444 ARG cc_start: 0.8464 (ttm110) cc_final: 0.7466 (tpt90) REVERT: H 483 GLU cc_start: 0.7822 (pt0) cc_final: 0.7447 (mt-10) REVERT: I 12 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.6846 (mtp180) REVERT: I 17 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7175 (tmt-80) REVERT: I 75 GLU cc_start: 0.8175 (tp30) cc_final: 0.7764 (tp30) REVERT: I 224 LYS cc_start: 0.6227 (ttpp) cc_final: 0.5702 (pttp) REVERT: I 306 MET cc_start: 0.4189 (mmp) cc_final: 0.3976 (mmp) REVERT: I 321 ARG cc_start: 0.7287 (ttm-80) cc_final: 0.7064 (ttm-80) REVERT: I 366 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: I 403 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7032 (ttp-170) REVERT: J 17 ARG cc_start: 0.8117 (ttp-110) cc_final: 0.7174 (tmt-80) REVERT: J 75 GLU cc_start: 0.8209 (tp30) cc_final: 0.7972 (tp30) REVERT: J 79 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7954 (ttpt) REVERT: J 165 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6897 (mtt) REVERT: J 193 GLN cc_start: 0.7671 (pt0) cc_final: 0.7389 (pt0) REVERT: J 224 LYS cc_start: 0.6292 (ttpp) cc_final: 0.5825 (pttp) REVERT: J 283 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6013 (mpp80) REVERT: J 306 MET cc_start: 0.4297 (mmp) cc_final: 0.4081 (mmp) REVERT: K 12 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.6815 (mtp180) REVERT: K 17 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7161 (tmt-80) REVERT: K 75 GLU cc_start: 0.8175 (tp30) cc_final: 0.7764 (tp30) REVERT: K 224 LYS cc_start: 0.6317 (ttpp) cc_final: 0.5930 (pttp) REVERT: K 400 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7075 (t-90) REVERT: K 403 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.6953 (ttp-110) REVERT: L 12 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.6921 (mtp180) REVERT: L 17 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7219 (tmt-80) REVERT: L 75 GLU cc_start: 0.8242 (tp30) cc_final: 0.7865 (tp30) REVERT: L 193 GLN cc_start: 0.7580 (pt0) cc_final: 0.7316 (pt0) REVERT: L 224 LYS cc_start: 0.6074 (ttpp) cc_final: 0.5688 (pttp) REVERT: L 283 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6007 (mpp80) REVERT: L 400 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.6999 (t-90) REVERT: M 12 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.6779 (mtp180) REVERT: M 17 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7166 (tmt-80) REVERT: M 75 GLU cc_start: 0.8163 (tp30) cc_final: 0.7680 (tp30) REVERT: M 224 LYS cc_start: 0.6275 (ttpp) cc_final: 0.5794 (pttp) REVERT: M 264 ASN cc_start: 0.5869 (OUTLIER) cc_final: 0.5590 (t0) REVERT: M 306 MET cc_start: 0.4349 (mmp) cc_final: 0.4044 (mmp) REVERT: M 400 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7079 (t-90) REVERT: M 403 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.6979 (ttp-170) REVERT: M 444 ARG cc_start: 0.8499 (ttm110) cc_final: 0.7293 (tpt90) REVERT: M 483 GLU cc_start: 0.7809 (pt0) cc_final: 0.7382 (mt-10) REVERT: N 17 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7211 (tmt-80) REVERT: N 75 GLU cc_start: 0.8254 (tp30) cc_final: 0.7721 (tp30) REVERT: N 79 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7784 (mtpt) REVERT: N 224 LYS cc_start: 0.6125 (ttpp) cc_final: 0.5664 (pttp) REVERT: N 400 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7177 (t-90) REVERT: N 403 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.7049 (ttp-170) outliers start: 223 outliers final: 142 residues processed: 1056 average time/residue: 1.3333 time to fit residues: 1788.4974 Evaluate side-chains 1061 residues out of total 5824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 888 time to evaluate : 4.495 ------------------------------------------------------------------------------- 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 419 ILE Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 168 VAL 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 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 176 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 209 THR 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 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 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 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 186 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 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 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 232 MET 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 400 HIS Chi-restraints excluded: chain G residue 419 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 386 VAL Chi-restraints excluded: chain H residue 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 168 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain I residue 368 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 165 MET Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 209 THR 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 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 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 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 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 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 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 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 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 176 VAL Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 368 VAL Chi-restraints excluded: chain N residue 400 HIS Chi-restraints excluded: chain N residue 419 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 40 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 675 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 374 optimal weight: 0.6980 chunk 534 optimal weight: 9.9990 chunk 628 optimal weight: 0.2980 chunk 409 optimal weight: 0.9980 chunk 537 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 H 365 GLN J 365 GLN K 365 GLN L 365 GLN M 365 GLN N 365 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.208079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127949 restraints weight = 55255.757| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.70 r_work: 0.3303 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3237 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= 0.178 Angle : 0.553 9.961 75712 Z= 0.288 Chirality : 0.041 0.165 9142 Planarity : 0.003 0.032 9884 Dihedral : 4.266 51.054 7928 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Rotamer: Outliers : 4.02 % Allowed : 25.82 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.10), residues: 7462 helix: 2.21 (0.08), residues: 4242 sheet: -0.95 (0.19), residues: 826 loop : -0.41 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP Q 23 HIS 0.002 0.001 HIS C 400 PHE 0.005 0.001 PHE I 65 TYR 0.010 0.001 TYR C 505 ARG 0.005 0.000 ARG E 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 55298.02 seconds wall clock time: 941 minutes 28.05 seconds (56488.05 seconds total)