Starting phenix.real_space_refine on Sat Sep 28 19:00:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/09_2024/7pko_13474.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/09_2024/7pko_13474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/09_2024/7pko_13474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/09_2024/7pko_13474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/09_2024/7pko_13474.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pko_13474/09_2024/7pko_13474.cif" } resolution = 3.9 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= 0.007 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 120 5.16 5 C 13064 2.51 5 N 3456 2.21 5 O 3728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20368 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "B" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "C" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "D" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "E" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "F" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "G" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "U" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2546 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Time building chain proxies: 12.13, per 1000 atoms: 0.60 Number of scatterers: 20368 At special positions: 0 Unit cell: (135.255, 135.255, 109.695, 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 120 16.00 O 3728 8.00 N 3456 7.00 C 13064 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: 5.24 Conformation dependent library (CDL) restraints added in 2.6 seconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 27 sheets defined 46.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.759A pdb=" N THR A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.532A pdb=" N PHE A 57 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 59 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 89 removed outlier: 4.243A pdb=" N THR A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.726A pdb=" N LEU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.715A pdb=" N LEU A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 198 through 213 removed outlier: 3.920A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.583A pdb=" N HIS A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.689A pdb=" N GLY A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 291 removed outlier: 3.543A pdb=" N LYS A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'B' and resid 3 through 7 removed outlier: 3.660A pdb=" N PHE B 7 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 Processing helix chain 'B' and resid 54 through 61 removed outlier: 4.363A pdb=" N LYS B 59 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B 61 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 91 removed outlier: 4.255A pdb=" N THR B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.814A pdb=" N LEU B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.835A pdb=" N LEU B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 198 through 213 removed outlier: 3.944A pdb=" N VAL B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 250 removed outlier: 3.582A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.711A pdb=" N GLY B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.717A pdb=" N LYS B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 23 through 32 removed outlier: 3.569A pdb=" N THR C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 61 removed outlier: 3.529A pdb=" N PHE C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS C 59 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 91 removed outlier: 4.101A pdb=" N THR C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.683A pdb=" N LEU C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 198 through 213 removed outlier: 3.922A pdb=" N VAL C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 250 removed outlier: 4.484A pdb=" N ALA C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.748A pdb=" N GLY C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.720A pdb=" N LYS C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 289 " --> pdb=" O CYS C 285 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE C 290 " --> pdb=" O LYS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 311 Processing helix chain 'D' and resid 3 through 6 Processing helix chain 'D' and resid 23 through 32 removed outlier: 3.885A pdb=" N THR D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 removed outlier: 4.497A pdb=" N LYS D 59 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 removed outlier: 4.163A pdb=" N THR D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.774A pdb=" N LEU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 removed outlier: 4.148A pdb=" N HIS D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 198 through 213 removed outlier: 3.954A pdb=" N VAL D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 250 removed outlier: 3.588A pdb=" N HIS D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 248 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.750A pdb=" N LYS D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 289 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 removed outlier: 3.755A pdb=" N VAL D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 33 removed outlier: 3.751A pdb=" N THR E 32 " --> pdb=" O LYS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 60 removed outlier: 4.555A pdb=" N LYS E 59 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 89 removed outlier: 4.273A pdb=" N THR E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.673A pdb=" N LEU E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.704A pdb=" N LEU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 128 through 141 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 199 through 213 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 247 removed outlier: 4.346A pdb=" N THR E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 279 removed outlier: 3.557A pdb=" N GLY E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 303 through 311 Processing helix chain 'F' and resid 3 through 7 removed outlier: 3.639A pdb=" N PHE F 7 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 32 removed outlier: 3.791A pdb=" N THR F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 61 removed outlier: 3.545A pdb=" N PHE F 57 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS F 59 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR F 61 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 91 removed outlier: 4.064A pdb=" N THR F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER F 90 " --> pdb=" O GLU F 86 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.863A pdb=" N LEU F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 120 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 141 removed outlier: 3.540A pdb=" N LEU F 132 " --> pdb=" O SER F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 198 through 213 removed outlier: 3.937A pdb=" N VAL F 202 " --> pdb=" O SER F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 250 removed outlier: 3.603A pdb=" N ASP F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 279 removed outlier: 3.751A pdb=" N GLY F 279 " --> pdb=" O SER F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.980A pdb=" N LYS F 286 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU F 288 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE F 290 " --> pdb=" O LYS F 286 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 311 Processing helix chain 'G' and resid 5 through 7 No H-bonds generated for 'chain 'G' and resid 5 through 7' Processing helix chain 'G' and resid 23 through 32 removed outlier: 3.564A pdb=" N THR G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 61 removed outlier: 3.618A pdb=" N PHE G 57 " --> pdb=" O PRO G 54 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS G 59 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR G 61 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 91 removed outlier: 4.110A pdb=" N THR G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER G 90 " --> pdb=" O GLU G 86 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 102 Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.719A pdb=" N LEU G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 117 " --> pdb=" O ASN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 141 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'G' and resid 199 through 213 Processing helix chain 'G' and resid 230 through 250 removed outlier: 4.483A pdb=" N ALA G 235 " --> pdb=" O TYR G 231 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR G 244 " --> pdb=" O ARG G 240 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN G 248 " --> pdb=" O THR G 244 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS G 250 " --> pdb=" O LYS G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 279 removed outlier: 3.776A pdb=" N GLY G 279 " --> pdb=" O SER G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 291 removed outlier: 3.528A pdb=" N LYS G 286 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU G 288 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU G 289 " --> pdb=" O CYS G 285 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE G 290 " --> pdb=" O LYS G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 311 Processing helix chain 'U' and resid 3 through 6 Processing helix chain 'U' and resid 23 through 32 removed outlier: 3.683A pdb=" N THR U 32 " --> pdb=" O LYS U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 61 removed outlier: 4.492A pdb=" N LYS U 59 " --> pdb=" O GLN U 56 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR U 61 " --> pdb=" O LYS U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 89 Processing helix chain 'U' and resid 97 through 102 removed outlier: 3.726A pdb=" N LEU U 102 " --> pdb=" O VAL U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 120 removed outlier: 3.699A pdb=" N LEU U 111 " --> pdb=" O SER U 107 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN U 120 " --> pdb=" O ILE U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 141 Processing helix chain 'U' and resid 199 through 213 Processing helix chain 'U' and resid 230 through 250 removed outlier: 4.508A pdb=" N ALA U 235 " --> pdb=" O TYR U 231 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN U 236 " --> pdb=" O SER U 232 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR U 244 " --> pdb=" O ARG U 240 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE U 245 " --> pdb=" O VAL U 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN U 248 " --> pdb=" O THR U 244 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS U 250 " --> pdb=" O LYS U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 Processing helix chain 'U' and resid 282 through 291 removed outlier: 3.687A pdb=" N LYS U 286 " --> pdb=" O LEU U 282 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU U 288 " --> pdb=" O VAL U 284 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU U 289 " --> pdb=" O CYS U 285 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE U 290 " --> pdb=" O LYS U 286 " (cutoff:3.500A) Processing helix chain 'U' and resid 303 through 312 removed outlier: 3.519A pdb=" N VAL U 312 " --> pdb=" O LYS U 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.519A pdb=" N SER A 46 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.717A pdb=" N ILE A 157 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS A 168 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 159 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU A 186 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AA5, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.514A pdb=" N SER B 46 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.507A pdb=" N ILE B 157 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B 168 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 159 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 186 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 8 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 46 Processing sheet with id=AA9, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.595A pdb=" N ILE C 157 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS C 168 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 159 " --> pdb=" O MET C 166 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU C 186 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 217 through 220 removed outlier: 3.510A pdb=" N VAL C 229 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 8 through 12 Processing sheet with id=AB3, first strand: chain 'D' and resid 44 through 46 Processing sheet with id=AB4, first strand: chain 'D' and resid 156 through 160 removed outlier: 6.387A pdb=" N ILE D 157 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS D 168 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE D 159 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU D 186 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AB6, first strand: chain 'E' and resid 8 through 12 Processing sheet with id=AB7, first strand: chain 'E' and resid 44 through 46 Processing sheet with id=AB8, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.421A pdb=" N ILE E 157 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS E 168 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE E 159 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU E 186 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AC1, first strand: chain 'F' and resid 44 through 46 Processing sheet with id=AC2, first strand: chain 'F' and resid 156 through 160 removed outlier: 6.475A pdb=" N ILE F 157 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS F 168 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE F 159 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU F 186 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 2 through 3 Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AC5, first strand: chain 'G' and resid 44 through 46 Processing sheet with id=AC6, first strand: chain 'G' and resid 156 through 160 removed outlier: 6.484A pdb=" N ILE G 157 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS G 168 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE G 159 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU G 186 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 8 through 12 Processing sheet with id=AC8, first strand: chain 'U' and resid 44 through 46 removed outlier: 3.712A pdb=" N SER U 46 " --> pdb=" O GLY U 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 156 through 160 removed outlier: 6.280A pdb=" N ILE U 157 " --> pdb=" O LYS U 168 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS U 168 " --> pdb=" O ILE U 157 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE U 159 " --> pdb=" O MET U 166 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU U 186 " --> pdb=" O LEU U 169 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2160 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: 5.96 Time building geometry restraints manager: 6.09 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: 6516 1.34 - 1.46: 4261 1.46 - 1.58: 9815 1.58 - 1.69: 0 1.69 - 1.81: 208 Bond restraints: 20800 Sorted by residual: bond pdb=" CA SER D 232 " pdb=" C SER D 232 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.34e-02 5.57e+03 5.83e+00 bond pdb=" CA SER A 232 " pdb=" C SER A 232 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.34e-02 5.57e+03 5.71e+00 bond pdb=" CA ARG U 210 " pdb=" C ARG U 210 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.72e-02 3.38e+03 5.44e+00 bond pdb=" CA ARG E 210 " pdb=" C ARG E 210 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.31e+00 bond pdb=" C ILE D 264 " pdb=" N ILE D 265 " ideal model delta sigma weight residual 1.334 1.312 0.022 1.29e-02 6.01e+03 2.89e+00 ... (remaining 20795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 26684 1.38 - 2.76: 1207 2.76 - 4.14: 149 4.14 - 5.52: 40 5.52 - 6.90: 8 Bond angle restraints: 28088 Sorted by residual: angle pdb=" C GLN A 160 " pdb=" N ASN A 161 " pdb=" CA ASN A 161 " ideal model delta sigma weight residual 121.90 116.31 5.59 1.26e+00 6.30e-01 1.97e+01 angle pdb=" C GLN D 160 " pdb=" N ASN D 161 " pdb=" CA ASN D 161 " ideal model delta sigma weight residual 121.90 116.60 5.30 1.26e+00 6.30e-01 1.77e+01 angle pdb=" C GLN C 160 " pdb=" N ASN C 161 " pdb=" CA ASN C 161 " ideal model delta sigma weight residual 121.90 116.79 5.11 1.26e+00 6.30e-01 1.65e+01 angle pdb=" N ASP G 41 " pdb=" CA ASP G 41 " pdb=" C ASP G 41 " ideal model delta sigma weight residual 114.09 108.05 6.04 1.55e+00 4.16e-01 1.52e+01 angle pdb=" N ASP C 15 " pdb=" CA ASP C 15 " pdb=" C ASP C 15 " ideal model delta sigma weight residual 114.75 109.85 4.90 1.26e+00 6.30e-01 1.51e+01 ... (remaining 28083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 11396 17.70 - 35.39: 1012 35.39 - 53.09: 158 53.09 - 70.78: 55 70.78 - 88.48: 27 Dihedral angle restraints: 12648 sinusoidal: 5208 harmonic: 7440 Sorted by residual: dihedral pdb=" CA MET G 40 " pdb=" C MET G 40 " pdb=" N ASP G 41 " pdb=" CA ASP G 41 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TYR G 17 " pdb=" C TYR G 17 " pdb=" N LYS G 18 " pdb=" CA LYS G 18 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N ILE C 47 " pdb=" CA ILE C 47 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 12645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2051 0.037 - 0.073: 859 0.073 - 0.110: 206 0.110 - 0.147: 19 0.147 - 0.183: 1 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CB THR U 170 " pdb=" CA THR U 170 " pdb=" OG1 THR U 170 " pdb=" CG2 THR U 170 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA ILE G 228 " pdb=" N ILE G 228 " pdb=" C ILE G 228 " pdb=" CB ILE G 228 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE U 228 " pdb=" N ILE U 228 " pdb=" C ILE U 228 " pdb=" CB ILE U 228 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 3133 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 294 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C 295 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 231 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C TYR E 231 " 0.023 2.00e-02 2.50e+03 pdb=" O TYR E 231 " -0.009 2.00e-02 2.50e+03 pdb=" N SER E 232 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 231 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C TYR F 231 " 0.023 2.00e-02 2.50e+03 pdb=" O TYR F 231 " -0.009 2.00e-02 2.50e+03 pdb=" N SER F 232 " -0.008 2.00e-02 2.50e+03 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2359 2.74 - 3.28: 21218 3.28 - 3.82: 31813 3.82 - 4.36: 37885 4.36 - 4.90: 62861 Nonbonded interactions: 156136 Sorted by model distance: nonbonded pdb=" OE2 GLU E 13 " pdb=" OG SER E 16 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR E 231 " pdb=" NZ LYS U 308 " model vdw 2.259 3.120 nonbonded pdb=" ND2 ASN C 62 " pdb=" OD1 ASN C 71 " model vdw 2.265 3.120 nonbonded pdb=" ND2 ASN G 62 " pdb=" OD1 ASN G 71 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN A 161 " pdb=" ND1 HIS A 201 " model vdw 2.269 3.120 ... (remaining 156131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'U' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.930 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: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 45.200 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 0.040 20800 Z= 0.258 Angle : 0.659 6.897 28088 Z= 0.400 Chirality : 0.040 0.183 3136 Planarity : 0.003 0.034 3560 Dihedral : 14.592 88.477 7800 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % 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: -4.16 (0.13), residues: 2488 helix: -2.31 (0.13), residues: 800 sheet: -2.74 (0.25), residues: 280 loop : -3.15 (0.14), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 266 HIS 0.003 0.001 HIS F 110 PHE 0.018 0.001 PHE D 257 TYR 0.017 0.002 TYR B 242 ARG 0.003 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8367 (mmt) cc_final: 0.7493 (mmt) REVERT: A 94 THR cc_start: 0.8378 (p) cc_final: 0.8169 (p) REVERT: A 142 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8512 (mp10) REVERT: A 144 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8313 (tppt) REVERT: A 262 GLN cc_start: 0.8353 (pt0) cc_final: 0.8082 (pp30) REVERT: B 76 MET cc_start: 0.8452 (mmt) cc_final: 0.7235 (mmt) REVERT: B 133 LEU cc_start: 0.9318 (tt) cc_final: 0.9080 (tt) REVERT: B 153 GLU cc_start: 0.8509 (tt0) cc_final: 0.8113 (tt0) REVERT: B 293 MET cc_start: 0.6085 (tmm) cc_final: 0.5564 (tmm) REVERT: C 59 LYS cc_start: 0.8911 (ptpp) cc_final: 0.8273 (ttpt) REVERT: C 76 MET cc_start: 0.8378 (mmt) cc_final: 0.7113 (mmt) REVERT: C 144 LYS cc_start: 0.7729 (tptp) cc_final: 0.7404 (tppt) REVERT: C 161 ASN cc_start: 0.8168 (p0) cc_final: 0.7867 (p0) REVERT: C 287 ARG cc_start: 0.8370 (mpt180) cc_final: 0.8099 (mpt180) REVERT: D 76 MET cc_start: 0.8355 (mmt) cc_final: 0.7377 (mmt) REVERT: D 112 GLU cc_start: 0.8630 (tp30) cc_final: 0.7955 (tp30) REVERT: D 144 LYS cc_start: 0.7866 (tppt) cc_final: 0.7151 (tppt) REVERT: D 183 ASN cc_start: 0.9353 (t0) cc_final: 0.9098 (t0) REVERT: D 276 MET cc_start: 0.7683 (ttm) cc_final: 0.7452 (ttm) REVERT: D 287 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8406 (mpt180) REVERT: E 34 LYS cc_start: 0.8398 (tptt) cc_final: 0.8123 (ttmm) REVERT: E 56 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8514 (tp40) REVERT: E 122 GLN cc_start: 0.9270 (mm-40) cc_final: 0.8815 (mm-40) REVERT: E 142 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8755 (mp10) REVERT: E 144 LYS cc_start: 0.7895 (tppt) cc_final: 0.7040 (tppt) REVERT: E 240 ARG cc_start: 0.8843 (ttp-170) cc_final: 0.8539 (ttp80) REVERT: E 262 GLN cc_start: 0.8318 (pt0) cc_final: 0.8083 (pp30) REVERT: E 287 ARG cc_start: 0.9070 (ttp-170) cc_final: 0.8513 (mmt90) REVERT: F 31 LEU cc_start: 0.9386 (tp) cc_final: 0.9178 (tt) REVERT: F 68 ARG cc_start: 0.8115 (mpp-170) cc_final: 0.7901 (tmt170) REVERT: F 76 MET cc_start: 0.8461 (mmt) cc_final: 0.7522 (mmt) REVERT: F 82 MET cc_start: 0.7509 (tpt) cc_final: 0.7124 (tpt) REVERT: F 104 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8464 (tpp80) REVERT: F 112 GLU cc_start: 0.8402 (tp30) cc_final: 0.7935 (tp30) REVERT: F 144 LYS cc_start: 0.8167 (tppt) cc_final: 0.7931 (tppt) REVERT: F 186 GLU cc_start: 0.8180 (tt0) cc_final: 0.7879 (tt0) REVERT: F 293 MET cc_start: 0.5661 (tmm) cc_final: 0.4268 (ptt) REVERT: G 56 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8559 (tp40) REVERT: G 58 LYS cc_start: 0.9356 (ttpt) cc_final: 0.9112 (ttmm) REVERT: G 66 ASN cc_start: 0.8338 (p0) cc_final: 0.8006 (p0) REVERT: G 76 MET cc_start: 0.8431 (mmt) cc_final: 0.7170 (mmt) REVERT: G 82 MET cc_start: 0.7474 (tpt) cc_final: 0.7059 (tpt) REVERT: G 144 LYS cc_start: 0.7958 (tppt) cc_final: 0.7535 (tppt) REVERT: G 184 PHE cc_start: 0.8739 (t80) cc_final: 0.8442 (t80) REVERT: G 186 GLU cc_start: 0.8107 (tt0) cc_final: 0.7639 (mt-10) REVERT: U 22 PHE cc_start: 0.8382 (m-80) cc_final: 0.7914 (m-80) REVERT: U 66 ASN cc_start: 0.7503 (t0) cc_final: 0.6292 (p0) REVERT: U 76 MET cc_start: 0.8645 (mmt) cc_final: 0.7741 (mmt) REVERT: U 113 ASN cc_start: 0.9213 (t0) cc_final: 0.8828 (m-40) REVERT: U 144 LYS cc_start: 0.8111 (tppt) cc_final: 0.7470 (tppt) REVERT: U 153 GLU cc_start: 0.8815 (pt0) cc_final: 0.8396 (pt0) REVERT: U 250 LYS cc_start: 0.7577 (mtpt) cc_final: 0.7052 (mmtt) outliers start: 0 outliers final: 0 residues processed: 549 average time/residue: 0.3715 time to fit residues: 292.9701 Evaluate side-chains 435 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 118 optimal weight: 0.0070 chunk 144 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 64 ASN A 71 ASN A 110 HIS A 142 GLN ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 110 HIS B 122 GLN B 142 GLN B 192 ASN ** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN C 14 ASN C 56 GLN C 64 ASN C 122 GLN C 142 GLN C 175 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 89 ASN D 110 HIS D 142 GLN D 183 ASN D 214 ASN D 237 HIS E 23 ASN E 71 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS E 142 GLN E 174 HIS E 237 HIS E 278 GLN E 280 ASN F 23 ASN F 89 ASN F 100 ASN F 142 GLN F 221 HIS G 14 ASN G 23 ASN G 56 GLN ** G 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN G 298 ASN ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 64 ASN U 71 ASN U 95 GLN U 110 HIS U 142 GLN U 175 GLN U 183 ASN ** U 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20800 Z= 0.162 Angle : 0.548 7.496 28088 Z= 0.291 Chirality : 0.040 0.146 3136 Planarity : 0.004 0.068 3560 Dihedral : 4.828 65.263 2688 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.29 % Allowed : 13.34 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.15), residues: 2488 helix: -0.36 (0.17), residues: 832 sheet: -2.52 (0.25), residues: 296 loop : -2.29 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 211 HIS 0.003 0.001 HIS C 237 PHE 0.015 0.001 PHE B 272 TYR 0.018 0.001 TYR E 242 ARG 0.005 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 469 time to evaluate : 2.525 Fit side-chains REVERT: A 76 MET cc_start: 0.8424 (mmt) cc_final: 0.7569 (mmt) REVERT: A 92 LYS cc_start: 0.8386 (tppt) cc_final: 0.8101 (tmtt) REVERT: A 135 SER cc_start: 0.9410 (t) cc_final: 0.9149 (p) REVERT: A 144 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8303 (tppt) REVERT: A 262 GLN cc_start: 0.8330 (pt0) cc_final: 0.8024 (pp30) REVERT: B 22 PHE cc_start: 0.8337 (m-80) cc_final: 0.7951 (m-80) REVERT: B 76 MET cc_start: 0.8303 (mmt) cc_final: 0.7517 (mmt) REVERT: B 92 LYS cc_start: 0.8358 (tppt) cc_final: 0.8093 (tmtt) REVERT: B 293 MET cc_start: 0.6067 (tmm) cc_final: 0.5774 (tmm) REVERT: C 59 LYS cc_start: 0.8837 (ptpp) cc_final: 0.8282 (ttpt) REVERT: C 60 ARG cc_start: 0.8921 (ttm170) cc_final: 0.7890 (ttp-110) REVERT: C 76 MET cc_start: 0.8311 (mmt) cc_final: 0.7326 (mmt) REVERT: C 112 GLU cc_start: 0.8624 (tp30) cc_final: 0.7840 (tp30) REVERT: C 144 LYS cc_start: 0.7631 (tptp) cc_final: 0.7000 (tppt) REVERT: C 161 ASN cc_start: 0.7863 (p0) cc_final: 0.7558 (p0) REVERT: C 309 MET cc_start: 0.7931 (mpp) cc_final: 0.7700 (mpp) REVERT: D 22 PHE cc_start: 0.8437 (m-80) cc_final: 0.8104 (m-80) REVERT: D 76 MET cc_start: 0.8294 (mmt) cc_final: 0.7333 (mmt) REVERT: D 144 LYS cc_start: 0.7844 (tppt) cc_final: 0.7066 (tppt) REVERT: D 153 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: D 183 ASN cc_start: 0.9326 (t0) cc_final: 0.9100 (t0) REVERT: D 287 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8165 (mmt90) REVERT: D 293 MET cc_start: 0.5227 (mtt) cc_final: 0.3823 (ttt) REVERT: D 309 MET cc_start: 0.7895 (mpp) cc_final: 0.7650 (mpp) REVERT: E 1 MET cc_start: 0.5004 (mmp) cc_final: 0.4164 (mpp) REVERT: E 22 PHE cc_start: 0.8479 (m-80) cc_final: 0.8051 (m-80) REVERT: E 56 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8427 (tp40) REVERT: E 76 MET cc_start: 0.8450 (mmt) cc_final: 0.7440 (mmt) REVERT: E 104 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8717 (tpp80) REVERT: E 122 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8840 (mm-40) REVERT: E 142 GLN cc_start: 0.8858 (mm110) cc_final: 0.8620 (mp10) REVERT: E 144 LYS cc_start: 0.7831 (tppt) cc_final: 0.6940 (tppt) REVERT: E 153 GLU cc_start: 0.8700 (pt0) cc_final: 0.8480 (pt0) REVERT: E 195 LYS cc_start: 0.9173 (ptpt) cc_final: 0.8881 (mtmt) REVERT: E 262 GLN cc_start: 0.8173 (pt0) cc_final: 0.7960 (pp30) REVERT: E 287 ARG cc_start: 0.9051 (ttp-170) cc_final: 0.8562 (mpt180) REVERT: F 31 LEU cc_start: 0.9289 (tp) cc_final: 0.9048 (tt) REVERT: F 76 MET cc_start: 0.8478 (mmt) cc_final: 0.7400 (mmt) REVERT: F 82 MET cc_start: 0.7552 (tpt) cc_final: 0.7174 (tpt) REVERT: F 144 LYS cc_start: 0.8047 (tppt) cc_final: 0.7741 (tppt) REVERT: G 56 GLN cc_start: 0.8902 (tp40) cc_final: 0.8508 (tp40) REVERT: G 57 PHE cc_start: 0.8642 (m-10) cc_final: 0.8054 (m-80) REVERT: G 66 ASN cc_start: 0.8384 (p0) cc_final: 0.8128 (p0) REVERT: G 76 MET cc_start: 0.8418 (mmt) cc_final: 0.7252 (mmt) REVERT: G 82 MET cc_start: 0.7290 (tpt) cc_final: 0.6899 (tpt) REVERT: G 144 LYS cc_start: 0.7875 (tppt) cc_final: 0.7412 (tppt) REVERT: G 186 GLU cc_start: 0.7953 (tt0) cc_final: 0.7452 (mt-10) REVERT: U 66 ASN cc_start: 0.7502 (t0) cc_final: 0.6257 (p0) REVERT: U 76 MET cc_start: 0.8206 (mmt) cc_final: 0.7220 (mmt) REVERT: U 104 ARG cc_start: 0.9017 (tpp80) cc_final: 0.8563 (tpp80) REVERT: U 144 LYS cc_start: 0.8050 (tppt) cc_final: 0.7308 (tppt) REVERT: U 153 GLU cc_start: 0.8829 (pt0) cc_final: 0.8548 (pt0) REVERT: U 215 LYS cc_start: 0.9179 (ttpp) cc_final: 0.8931 (ttpt) REVERT: U 240 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8149 (ttp80) REVERT: U 309 MET cc_start: 0.7928 (mpp) cc_final: 0.7618 (mpp) outliers start: 52 outliers final: 29 residues processed: 486 average time/residue: 0.3417 time to fit residues: 245.6562 Evaluate side-chains 446 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 416 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 239 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 243 optimal weight: 0.6980 chunk 200 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS B 258 ASN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN E 278 GLN F 62 ASN G 192 ASN U 23 ASN U 237 HIS U 291 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20800 Z= 0.255 Angle : 0.566 7.455 28088 Z= 0.295 Chirality : 0.041 0.209 3136 Planarity : 0.003 0.047 3560 Dihedral : 4.606 60.362 2688 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.39 % Allowed : 14.92 % Favored : 81.69 % 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: -1.98 (0.16), residues: 2488 helix: 0.07 (0.17), residues: 832 sheet: -2.27 (0.26), residues: 296 loop : -2.03 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 269 HIS 0.003 0.001 HIS A 201 PHE 0.020 0.001 PHE A 22 TYR 0.017 0.002 TYR E 226 ARG 0.005 0.000 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 434 time to evaluate : 2.486 Fit side-chains REVERT: A 76 MET cc_start: 0.8581 (mmt) cc_final: 0.8330 (mpp) REVERT: A 92 LYS cc_start: 0.8420 (tppt) cc_final: 0.8174 (tmtt) REVERT: A 135 SER cc_start: 0.9488 (t) cc_final: 0.9158 (p) REVERT: A 144 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8307 (tppt) REVERT: A 262 GLN cc_start: 0.8213 (pt0) cc_final: 0.7962 (pp30) REVERT: A 293 MET cc_start: 0.5474 (tmm) cc_final: 0.5168 (tmm) REVERT: B 76 MET cc_start: 0.8406 (mmt) cc_final: 0.7557 (mmt) REVERT: B 92 LYS cc_start: 0.8354 (tppt) cc_final: 0.8107 (tmtt) REVERT: B 293 MET cc_start: 0.6075 (tmm) cc_final: 0.5872 (tmm) REVERT: C 59 LYS cc_start: 0.8847 (ptpp) cc_final: 0.8289 (ttpt) REVERT: C 76 MET cc_start: 0.8407 (mmt) cc_final: 0.7414 (mmt) REVERT: C 112 GLU cc_start: 0.8644 (tp30) cc_final: 0.8018 (tp30) REVERT: C 144 LYS cc_start: 0.7663 (tptp) cc_final: 0.7038 (tppt) REVERT: C 309 MET cc_start: 0.7798 (mpp) cc_final: 0.7336 (mpp) REVERT: D 22 PHE cc_start: 0.8550 (m-80) cc_final: 0.8307 (m-80) REVERT: D 76 MET cc_start: 0.8281 (mmt) cc_final: 0.7377 (mmt) REVERT: D 123 ASP cc_start: 0.8273 (t0) cc_final: 0.7966 (m-30) REVERT: D 144 LYS cc_start: 0.7933 (tppt) cc_final: 0.7134 (tppt) REVERT: D 153 GLU cc_start: 0.8467 (pt0) cc_final: 0.8125 (pm20) REVERT: D 183 ASN cc_start: 0.9337 (t0) cc_final: 0.9119 (t0) REVERT: D 287 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8166 (mmt90) REVERT: D 309 MET cc_start: 0.7916 (mpp) cc_final: 0.7692 (mpp) REVERT: E 1 MET cc_start: 0.5032 (mmp) cc_final: 0.4147 (mpp) REVERT: E 56 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8463 (tp40) REVERT: E 76 MET cc_start: 0.8453 (mmt) cc_final: 0.7408 (mmt) REVERT: E 104 ARG cc_start: 0.9153 (tpp80) cc_final: 0.8816 (tpp80) REVERT: E 122 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8785 (mm-40) REVERT: E 142 GLN cc_start: 0.8923 (mm110) cc_final: 0.8520 (mp10) REVERT: E 144 LYS cc_start: 0.7897 (tppt) cc_final: 0.7007 (tppt) REVERT: E 153 GLU cc_start: 0.8844 (pt0) cc_final: 0.8600 (pt0) REVERT: E 195 LYS cc_start: 0.9234 (ptpt) cc_final: 0.8905 (mtmt) REVERT: E 240 ARG cc_start: 0.8551 (ttm170) cc_final: 0.8242 (ttp80) REVERT: E 287 ARG cc_start: 0.9060 (ttp-170) cc_final: 0.8499 (mmt180) REVERT: E 293 MET cc_start: 0.6069 (tmm) cc_final: 0.5589 (tmm) REVERT: F 76 MET cc_start: 0.8520 (mmt) cc_final: 0.7453 (mmt) REVERT: F 82 MET cc_start: 0.7622 (tpt) cc_final: 0.7256 (tpt) REVERT: F 144 LYS cc_start: 0.8053 (tppt) cc_final: 0.7755 (tppt) REVERT: G 56 GLN cc_start: 0.8948 (tp40) cc_final: 0.8539 (tp40) REVERT: G 57 PHE cc_start: 0.8677 (m-10) cc_final: 0.7998 (m-80) REVERT: G 66 ASN cc_start: 0.8537 (p0) cc_final: 0.8246 (p0) REVERT: G 70 MET cc_start: 0.7225 (mtm) cc_final: 0.6933 (mtt) REVERT: G 76 MET cc_start: 0.8421 (mmt) cc_final: 0.7646 (mmt) REVERT: G 82 MET cc_start: 0.7402 (tpt) cc_final: 0.6955 (tpt) REVERT: G 104 ARG cc_start: 0.9032 (ttm-80) cc_final: 0.8476 (tpp80) REVERT: G 142 GLN cc_start: 0.8899 (mm110) cc_final: 0.8435 (mp10) REVERT: G 144 LYS cc_start: 0.7916 (tppt) cc_final: 0.7428 (tppt) REVERT: G 186 GLU cc_start: 0.8067 (tt0) cc_final: 0.7526 (mt-10) REVERT: U 66 ASN cc_start: 0.7687 (t0) cc_final: 0.6528 (p0) REVERT: U 76 MET cc_start: 0.8282 (mmt) cc_final: 0.7272 (mmt) REVERT: U 144 LYS cc_start: 0.8034 (tppt) cc_final: 0.7330 (tppt) REVERT: U 183 ASN cc_start: 0.8955 (t0) cc_final: 0.8468 (t0) REVERT: U 240 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8492 (ttm110) REVERT: U 309 MET cc_start: 0.7961 (mpp) cc_final: 0.7649 (mpp) outliers start: 77 outliers final: 54 residues processed: 462 average time/residue: 0.3228 time to fit residues: 225.1841 Evaluate side-chains 469 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 415 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 276 MET Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 71 ASN ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 278 GLN ** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 212 GLN U 221 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20800 Z= 0.381 Angle : 0.633 7.248 28088 Z= 0.328 Chirality : 0.043 0.175 3136 Planarity : 0.004 0.047 3560 Dihedral : 4.766 56.122 2688 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.53 % Allowed : 15.89 % Favored : 79.58 % 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: -1.85 (0.16), residues: 2488 helix: 0.07 (0.17), residues: 832 sheet: -1.90 (0.27), residues: 280 loop : -1.96 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.004 0.001 HIS F 225 PHE 0.014 0.001 PHE E 272 TYR 0.019 0.002 TYR E 226 ARG 0.007 0.001 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 430 time to evaluate : 2.409 Fit side-chains REVERT: A 76 MET cc_start: 0.8612 (mmt) cc_final: 0.7876 (mmt) REVERT: A 92 LYS cc_start: 0.8397 (tppt) cc_final: 0.8190 (tmtt) REVERT: A 144 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8284 (tppt) REVERT: A 262 GLN cc_start: 0.8143 (pt0) cc_final: 0.7920 (pp30) REVERT: A 293 MET cc_start: 0.5419 (tmm) cc_final: 0.5056 (tmm) REVERT: B 76 MET cc_start: 0.8491 (mmt) cc_final: 0.7621 (mmt) REVERT: B 195 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8943 (mtmt) REVERT: B 293 MET cc_start: 0.6080 (tmm) cc_final: 0.5858 (tmm) REVERT: C 59 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8297 (ttpt) REVERT: C 76 MET cc_start: 0.8457 (mmt) cc_final: 0.7583 (mmt) REVERT: C 112 GLU cc_start: 0.8652 (tp30) cc_final: 0.8061 (tp30) REVERT: C 133 LEU cc_start: 0.9238 (tt) cc_final: 0.9019 (tt) REVERT: C 144 LYS cc_start: 0.7717 (tptp) cc_final: 0.7079 (tppt) REVERT: C 153 GLU cc_start: 0.8594 (pt0) cc_final: 0.8243 (pm20) REVERT: C 161 ASN cc_start: 0.8189 (p0) cc_final: 0.7782 (p0) REVERT: C 309 MET cc_start: 0.7800 (mpp) cc_final: 0.7282 (mpp) REVERT: D 76 MET cc_start: 0.8458 (mmt) cc_final: 0.7475 (mmt) REVERT: D 92 LYS cc_start: 0.8389 (tppt) cc_final: 0.8001 (tmtt) REVERT: D 123 ASP cc_start: 0.8381 (t0) cc_final: 0.8079 (m-30) REVERT: D 133 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8995 (tt) REVERT: D 144 LYS cc_start: 0.7920 (tppt) cc_final: 0.7163 (tppt) REVERT: D 183 ASN cc_start: 0.9321 (t0) cc_final: 0.9106 (t0) REVERT: D 240 ARG cc_start: 0.8652 (ttm170) cc_final: 0.8389 (ttm170) REVERT: D 287 ARG cc_start: 0.8700 (ttp80) cc_final: 0.8313 (mpt180) REVERT: D 309 MET cc_start: 0.8053 (mpp) cc_final: 0.7843 (mpp) REVERT: E 1 MET cc_start: 0.4956 (mmp) cc_final: 0.4120 (mpp) REVERT: E 34 LYS cc_start: 0.8546 (tptt) cc_final: 0.8344 (tptt) REVERT: E 76 MET cc_start: 0.8495 (mmt) cc_final: 0.7501 (mmt) REVERT: E 122 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8734 (mm-40) REVERT: E 142 GLN cc_start: 0.9123 (mm110) cc_final: 0.8721 (mp10) REVERT: E 144 LYS cc_start: 0.7792 (tppt) cc_final: 0.6995 (tppt) REVERT: E 153 GLU cc_start: 0.8921 (pt0) cc_final: 0.8673 (pt0) REVERT: E 195 LYS cc_start: 0.9300 (ptpt) cc_final: 0.8942 (mtmt) REVERT: E 287 ARG cc_start: 0.9044 (ttp-170) cc_final: 0.8530 (mpt180) REVERT: E 309 MET cc_start: 0.8072 (mpp) cc_final: 0.7427 (mpp) REVERT: F 76 MET cc_start: 0.8458 (mmt) cc_final: 0.7054 (mmt) REVERT: F 82 MET cc_start: 0.7673 (tpt) cc_final: 0.7307 (tpt) REVERT: F 144 LYS cc_start: 0.8019 (tppt) cc_final: 0.7566 (tppt) REVERT: F 287 ARG cc_start: 0.7701 (mmt90) cc_final: 0.7410 (mmt90) REVERT: G 9 TYR cc_start: 0.8042 (p90) cc_final: 0.7700 (p90) REVERT: G 56 GLN cc_start: 0.8936 (tp40) cc_final: 0.8576 (tp40) REVERT: G 57 PHE cc_start: 0.8707 (m-10) cc_final: 0.8035 (m-80) REVERT: G 66 ASN cc_start: 0.8526 (p0) cc_final: 0.8211 (p0) REVERT: G 76 MET cc_start: 0.8434 (mmt) cc_final: 0.7338 (mmt) REVERT: G 82 MET cc_start: 0.7568 (tpt) cc_final: 0.7138 (tpt) REVERT: G 142 GLN cc_start: 0.9037 (mm110) cc_final: 0.8558 (mp10) REVERT: G 144 LYS cc_start: 0.7986 (tppt) cc_final: 0.7514 (tppt) REVERT: G 186 GLU cc_start: 0.8190 (tt0) cc_final: 0.7637 (mt-10) REVERT: G 195 LYS cc_start: 0.9245 (ptpp) cc_final: 0.8867 (mtmt) REVERT: G 309 MET cc_start: 0.7937 (mpp) cc_final: 0.7343 (mpp) REVERT: U 66 ASN cc_start: 0.7784 (t0) cc_final: 0.7567 (p0) REVERT: U 76 MET cc_start: 0.8377 (mmt) cc_final: 0.7332 (mmt) REVERT: U 144 LYS cc_start: 0.8113 (tppt) cc_final: 0.7393 (tppt) REVERT: U 183 ASN cc_start: 0.9002 (t0) cc_final: 0.8526 (t0) REVERT: U 240 ARG cc_start: 0.8770 (ttm110) cc_final: 0.8543 (ttm170) REVERT: U 309 MET cc_start: 0.7990 (mpp) cc_final: 0.7679 (mpp) outliers start: 103 outliers final: 82 residues processed: 473 average time/residue: 0.3235 time to fit residues: 231.6878 Evaluate side-chains 495 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 412 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 135 SER Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 212 GLN Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 276 MET Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 178 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 71 ASN ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 GLN ** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20800 Z= 0.160 Angle : 0.531 8.739 28088 Z= 0.275 Chirality : 0.040 0.151 3136 Planarity : 0.003 0.049 3560 Dihedral : 4.394 50.345 2688 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.68 % Allowed : 18.09 % Favored : 79.23 % 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: -1.40 (0.16), residues: 2488 helix: 0.62 (0.18), residues: 832 sheet: -2.06 (0.27), residues: 296 loop : -1.69 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 211 HIS 0.002 0.001 HIS F 225 PHE 0.020 0.001 PHE D 22 TYR 0.012 0.001 TYR G 226 ARG 0.009 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 446 time to evaluate : 2.661 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8381 (mmt) cc_final: 0.7601 (mmt) REVERT: A 135 SER cc_start: 0.9453 (t) cc_final: 0.9108 (p) REVERT: A 144 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8269 (tppt) REVERT: A 153 GLU cc_start: 0.8236 (pt0) cc_final: 0.7886 (pm20) REVERT: A 262 GLN cc_start: 0.8081 (pt0) cc_final: 0.7852 (pp30) REVERT: A 293 MET cc_start: 0.5323 (tmm) cc_final: 0.4930 (tmm) REVERT: B 76 MET cc_start: 0.8340 (mmt) cc_final: 0.7503 (mmt) REVERT: B 195 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8828 (mtmt) REVERT: C 59 LYS cc_start: 0.8856 (ptpp) cc_final: 0.8247 (ttpt) REVERT: C 76 MET cc_start: 0.8405 (mmt) cc_final: 0.7413 (mmt) REVERT: C 112 GLU cc_start: 0.8664 (tp30) cc_final: 0.8043 (tp30) REVERT: C 144 LYS cc_start: 0.7641 (tptp) cc_final: 0.7024 (tppt) REVERT: C 309 MET cc_start: 0.7902 (mpp) cc_final: 0.7431 (mpp) REVERT: D 76 MET cc_start: 0.8276 (mmt) cc_final: 0.7357 (mmt) REVERT: D 92 LYS cc_start: 0.8400 (tppt) cc_final: 0.8043 (tmtt) REVERT: D 123 ASP cc_start: 0.8264 (t0) cc_final: 0.8025 (m-30) REVERT: D 133 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8991 (tt) REVERT: D 144 LYS cc_start: 0.7911 (tppt) cc_final: 0.7166 (tppt) REVERT: D 153 GLU cc_start: 0.8192 (pt0) cc_final: 0.7945 (pm20) REVERT: D 183 ASN cc_start: 0.9355 (t0) cc_final: 0.9129 (t0) REVERT: D 287 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8276 (mpt180) REVERT: D 309 MET cc_start: 0.8048 (mpp) cc_final: 0.7773 (mpp) REVERT: E 1 MET cc_start: 0.5036 (mmp) cc_final: 0.4210 (mpp) REVERT: E 76 MET cc_start: 0.8388 (mmt) cc_final: 0.7569 (mmt) REVERT: E 122 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8718 (mm-40) REVERT: E 142 GLN cc_start: 0.8877 (mm110) cc_final: 0.8551 (mp10) REVERT: E 144 LYS cc_start: 0.7877 (tppt) cc_final: 0.7071 (tppt) REVERT: E 195 LYS cc_start: 0.9249 (ptpt) cc_final: 0.8914 (mtmt) REVERT: E 287 ARG cc_start: 0.9025 (ttp-170) cc_final: 0.8501 (mpt180) REVERT: F 76 MET cc_start: 0.8444 (mmt) cc_final: 0.7432 (mmt) REVERT: F 82 MET cc_start: 0.7529 (tpt) cc_final: 0.7149 (tpt) REVERT: F 144 LYS cc_start: 0.8020 (tppt) cc_final: 0.7499 (tppt) REVERT: G 56 GLN cc_start: 0.8890 (tp40) cc_final: 0.8464 (tp40) REVERT: G 57 PHE cc_start: 0.8667 (m-10) cc_final: 0.8006 (m-80) REVERT: G 66 ASN cc_start: 0.8542 (p0) cc_final: 0.8244 (p0) REVERT: G 70 MET cc_start: 0.7215 (mtm) cc_final: 0.6968 (mtt) REVERT: G 76 MET cc_start: 0.8255 (mmt) cc_final: 0.7477 (mmt) REVERT: G 82 MET cc_start: 0.7463 (tpt) cc_final: 0.7019 (tpt) REVERT: G 142 GLN cc_start: 0.8862 (mm110) cc_final: 0.8473 (mp10) REVERT: G 144 LYS cc_start: 0.7802 (tppt) cc_final: 0.7326 (tppt) REVERT: G 147 GLU cc_start: 0.8244 (tt0) cc_final: 0.8018 (tt0) REVERT: G 195 LYS cc_start: 0.9152 (ptpp) cc_final: 0.8840 (mtmt) REVERT: U 66 ASN cc_start: 0.7198 (t0) cc_final: 0.5635 (p0) REVERT: U 76 MET cc_start: 0.8252 (mmt) cc_final: 0.7241 (mmt) REVERT: U 104 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8625 (tpp80) REVERT: U 113 ASN cc_start: 0.9307 (t0) cc_final: 0.8914 (m-40) REVERT: U 144 LYS cc_start: 0.8153 (tppt) cc_final: 0.7381 (tppt) REVERT: U 183 ASN cc_start: 0.8973 (t0) cc_final: 0.8695 (t0) REVERT: U 240 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8483 (ttm110) REVERT: U 287 ARG cc_start: 0.7825 (mmt90) cc_final: 0.7595 (mmt90) REVERT: U 309 MET cc_start: 0.7907 (mpp) cc_final: 0.7480 (mpp) outliers start: 61 outliers final: 49 residues processed: 474 average time/residue: 0.3270 time to fit residues: 234.1065 Evaluate side-chains 464 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 414 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 276 MET Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 239 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 0.1980 chunk 125 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20800 Z= 0.150 Angle : 0.538 9.097 28088 Z= 0.274 Chirality : 0.040 0.222 3136 Planarity : 0.003 0.040 3560 Dihedral : 4.199 45.703 2688 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.26 % Allowed : 18.84 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2488 helix: 0.89 (0.18), residues: 832 sheet: -1.97 (0.26), residues: 296 loop : -1.52 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.002 0.000 HIS C 110 PHE 0.010 0.001 PHE A 7 TYR 0.018 0.001 TYR F 61 ARG 0.006 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 447 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8437 (mmt) cc_final: 0.7732 (mmt) REVERT: A 135 SER cc_start: 0.9454 (t) cc_final: 0.9100 (p) REVERT: A 144 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8267 (tppt) REVERT: A 153 GLU cc_start: 0.8113 (pt0) cc_final: 0.7882 (pm20) REVERT: A 293 MET cc_start: 0.5386 (tmm) cc_final: 0.4948 (tmm) REVERT: B 22 PHE cc_start: 0.8269 (m-80) cc_final: 0.7852 (m-80) REVERT: B 76 MET cc_start: 0.8283 (mmt) cc_final: 0.7459 (mmt) REVERT: B 104 ARG cc_start: 0.9246 (tpp80) cc_final: 0.8828 (tpp80) REVERT: B 195 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8835 (mtmt) REVERT: B 309 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7536 (mpp) REVERT: C 59 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8272 (ttpt) REVERT: C 76 MET cc_start: 0.8384 (mmt) cc_final: 0.7437 (mmt) REVERT: C 112 GLU cc_start: 0.8661 (tp30) cc_final: 0.8094 (tp30) REVERT: C 144 LYS cc_start: 0.7555 (tptp) cc_final: 0.6947 (tppt) REVERT: C 153 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: C 309 MET cc_start: 0.7896 (mpp) cc_final: 0.7381 (mpp) REVERT: D 76 MET cc_start: 0.8212 (mmt) cc_final: 0.7365 (mmt) REVERT: D 123 ASP cc_start: 0.8196 (t0) cc_final: 0.7925 (m-30) REVERT: D 144 LYS cc_start: 0.7887 (tppt) cc_final: 0.7139 (tppt) REVERT: D 183 ASN cc_start: 0.9342 (t0) cc_final: 0.9114 (t0) REVERT: D 287 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8216 (mpt180) REVERT: D 309 MET cc_start: 0.8028 (mpp) cc_final: 0.7712 (mpp) REVERT: E 1 MET cc_start: 0.4656 (mmp) cc_final: 0.3951 (mpp) REVERT: E 22 PHE cc_start: 0.8357 (m-80) cc_final: 0.8107 (m-80) REVERT: E 56 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8246 (tm-30) REVERT: E 60 ARG cc_start: 0.8598 (ttm110) cc_final: 0.7880 (ttp-110) REVERT: E 76 MET cc_start: 0.8316 (mmt) cc_final: 0.7906 (mmt) REVERT: E 122 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8704 (mm-40) REVERT: E 142 GLN cc_start: 0.8846 (mm110) cc_final: 0.8547 (mp10) REVERT: E 144 LYS cc_start: 0.7873 (tppt) cc_final: 0.7074 (tppt) REVERT: E 195 LYS cc_start: 0.9242 (ptpt) cc_final: 0.8907 (mtmt) REVERT: E 287 ARG cc_start: 0.9018 (ttp-170) cc_final: 0.8416 (mmt180) REVERT: E 309 MET cc_start: 0.8002 (mpp) cc_final: 0.7794 (mpp) REVERT: F 76 MET cc_start: 0.8437 (mmt) cc_final: 0.7408 (mmt) REVERT: F 82 MET cc_start: 0.7508 (tpt) cc_final: 0.7131 (tpt) REVERT: F 104 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8588 (tpp80) REVERT: F 144 LYS cc_start: 0.8003 (tppt) cc_final: 0.7476 (tppt) REVERT: G 56 GLN cc_start: 0.8856 (tp40) cc_final: 0.8410 (tp40) REVERT: G 57 PHE cc_start: 0.8695 (m-10) cc_final: 0.7921 (m-80) REVERT: G 66 ASN cc_start: 0.8531 (p0) cc_final: 0.8255 (p0) REVERT: G 76 MET cc_start: 0.8254 (mmt) cc_final: 0.7508 (mmt) REVERT: G 82 MET cc_start: 0.7230 (tpt) cc_final: 0.6852 (tpt) REVERT: G 142 GLN cc_start: 0.8835 (mm110) cc_final: 0.8497 (mp10) REVERT: G 144 LYS cc_start: 0.7808 (tppt) cc_final: 0.7319 (tppt) REVERT: G 147 GLU cc_start: 0.8151 (tt0) cc_final: 0.7897 (tt0) REVERT: G 195 LYS cc_start: 0.9103 (ptpp) cc_final: 0.8803 (mtmt) REVERT: G 309 MET cc_start: 0.7696 (mpp) cc_final: 0.7156 (mpp) REVERT: U 57 PHE cc_start: 0.8758 (m-80) cc_final: 0.8170 (m-80) REVERT: U 66 ASN cc_start: 0.7424 (t0) cc_final: 0.6022 (p0) REVERT: U 76 MET cc_start: 0.8254 (mmt) cc_final: 0.7353 (mmt) REVERT: U 104 ARG cc_start: 0.9157 (tpp80) cc_final: 0.8649 (tpp80) REVERT: U 113 ASN cc_start: 0.9297 (t0) cc_final: 0.8910 (m-40) REVERT: U 144 LYS cc_start: 0.8129 (tppt) cc_final: 0.7405 (tppt) REVERT: U 183 ASN cc_start: 0.8886 (t0) cc_final: 0.8587 (t0) REVERT: U 195 LYS cc_start: 0.9278 (ptpp) cc_final: 0.9045 (mtmm) REVERT: U 240 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8482 (ttm110) REVERT: U 287 ARG cc_start: 0.7854 (mmt90) cc_final: 0.7577 (mmt90) REVERT: U 309 MET cc_start: 0.7910 (mpp) cc_final: 0.7556 (mpp) outliers start: 74 outliers final: 62 residues processed: 484 average time/residue: 0.3253 time to fit residues: 238.0237 Evaluate side-chains 486 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 422 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 276 MET Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN C 110 HIS ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 HIS E 278 GLN ** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20800 Z= 0.151 Angle : 0.539 9.224 28088 Z= 0.273 Chirality : 0.039 0.205 3136 Planarity : 0.003 0.036 3560 Dihedral : 3.994 38.774 2688 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.17 % Allowed : 19.89 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2488 helix: 1.21 (0.18), residues: 824 sheet: -1.90 (0.26), residues: 296 loop : -1.42 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 211 HIS 0.002 0.000 HIS A 201 PHE 0.011 0.001 PHE G 22 TYR 0.012 0.001 TYR A 61 ARG 0.006 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 444 time to evaluate : 2.726 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8476 (mmt) cc_final: 0.7820 (mmt) REVERT: A 135 SER cc_start: 0.9427 (t) cc_final: 0.9104 (p) REVERT: A 144 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8246 (tppt) REVERT: A 153 GLU cc_start: 0.8169 (pt0) cc_final: 0.7864 (pm20) REVERT: A 293 MET cc_start: 0.5053 (tmm) cc_final: 0.4685 (tmm) REVERT: A 309 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7583 (mpp) REVERT: B 22 PHE cc_start: 0.8236 (m-80) cc_final: 0.7821 (m-80) REVERT: B 70 MET cc_start: 0.6785 (mtm) cc_final: 0.6437 (mtt) REVERT: B 76 MET cc_start: 0.8284 (mmt) cc_final: 0.7537 (mmt) REVERT: B 104 ARG cc_start: 0.9220 (tpp80) cc_final: 0.8812 (tpp80) REVERT: B 309 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7618 (mpp) REVERT: C 59 LYS cc_start: 0.8819 (ptpp) cc_final: 0.8230 (ttmt) REVERT: C 76 MET cc_start: 0.8404 (mmt) cc_final: 0.7525 (mmt) REVERT: C 112 GLU cc_start: 0.8641 (tp30) cc_final: 0.8044 (tp30) REVERT: C 144 LYS cc_start: 0.7492 (tptp) cc_final: 0.6950 (tppt) REVERT: C 153 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: C 309 MET cc_start: 0.7982 (mpp) cc_final: 0.7452 (mpp) REVERT: D 60 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8303 (ttm-80) REVERT: D 76 MET cc_start: 0.8291 (mmt) cc_final: 0.7386 (mmt) REVERT: D 123 ASP cc_start: 0.8305 (t0) cc_final: 0.7978 (m-30) REVERT: D 144 LYS cc_start: 0.7837 (tppt) cc_final: 0.7117 (tppt) REVERT: D 183 ASN cc_start: 0.9294 (t0) cc_final: 0.9080 (t0) REVERT: D 195 LYS cc_start: 0.9094 (ptpt) cc_final: 0.8648 (mtmt) REVERT: D 287 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8033 (mmt90) REVERT: D 309 MET cc_start: 0.7974 (mpp) cc_final: 0.7632 (mpp) REVERT: E 1 MET cc_start: 0.4673 (mmp) cc_final: 0.3988 (mpp) REVERT: E 22 PHE cc_start: 0.8235 (m-80) cc_final: 0.7943 (m-80) REVERT: E 56 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8360 (tm-30) REVERT: E 76 MET cc_start: 0.8307 (mmt) cc_final: 0.7955 (mmt) REVERT: E 122 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8832 (mm-40) REVERT: E 142 GLN cc_start: 0.8830 (mm110) cc_final: 0.8584 (mp10) REVERT: E 144 LYS cc_start: 0.7827 (tppt) cc_final: 0.7031 (tppt) REVERT: E 172 LEU cc_start: 0.9360 (mt) cc_final: 0.8688 (tt) REVERT: E 195 LYS cc_start: 0.9243 (ptpt) cc_final: 0.8910 (mtmt) REVERT: E 212 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8593 (tm130) REVERT: E 287 ARG cc_start: 0.8986 (ttp-170) cc_final: 0.8381 (mmt180) REVERT: F 76 MET cc_start: 0.8387 (mmt) cc_final: 0.7421 (mmt) REVERT: F 82 MET cc_start: 0.7515 (tpt) cc_final: 0.7143 (tpt) REVERT: F 104 ARG cc_start: 0.8891 (tpp80) cc_final: 0.8640 (tpp80) REVERT: F 144 LYS cc_start: 0.7982 (tppt) cc_final: 0.7476 (tppt) REVERT: G 56 GLN cc_start: 0.8810 (tp40) cc_final: 0.8301 (tp40) REVERT: G 57 PHE cc_start: 0.8588 (m-10) cc_final: 0.7857 (m-80) REVERT: G 66 ASN cc_start: 0.8524 (p0) cc_final: 0.8264 (p0) REVERT: G 76 MET cc_start: 0.8249 (mmt) cc_final: 0.7517 (mmt) REVERT: G 82 MET cc_start: 0.7271 (tpt) cc_final: 0.6889 (tpt) REVERT: G 144 LYS cc_start: 0.7780 (tppt) cc_final: 0.7284 (tppt) REVERT: G 195 LYS cc_start: 0.9090 (ptpp) cc_final: 0.8737 (mtmt) REVERT: G 309 MET cc_start: 0.7723 (mpp) cc_final: 0.7518 (mpp) REVERT: U 57 PHE cc_start: 0.8775 (m-80) cc_final: 0.8117 (m-80) REVERT: U 66 ASN cc_start: 0.7444 (t0) cc_final: 0.6013 (p0) REVERT: U 76 MET cc_start: 0.8238 (mmt) cc_final: 0.7360 (mmt) REVERT: U 104 ARG cc_start: 0.9177 (tpp80) cc_final: 0.8657 (tpp80) REVERT: U 113 ASN cc_start: 0.9285 (t0) cc_final: 0.8850 (m-40) REVERT: U 144 LYS cc_start: 0.8117 (tppt) cc_final: 0.7385 (tppt) REVERT: U 183 ASN cc_start: 0.8896 (t0) cc_final: 0.8588 (t0) REVERT: U 240 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8512 (ttm110) REVERT: U 287 ARG cc_start: 0.7758 (mmt90) cc_final: 0.7447 (mmt90) REVERT: U 309 MET cc_start: 0.7985 (mpp) cc_final: 0.7669 (mpp) outliers start: 72 outliers final: 60 residues processed: 480 average time/residue: 0.3292 time to fit residues: 237.0910 Evaluate side-chains 485 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 421 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 276 MET Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 71 ASN ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 GLN G 183 ASN G 212 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20800 Z= 0.256 Angle : 0.578 8.996 28088 Z= 0.295 Chirality : 0.041 0.199 3136 Planarity : 0.003 0.034 3560 Dihedral : 4.091 35.583 2688 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.79 % Allowed : 20.03 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2488 helix: 1.10 (0.18), residues: 832 sheet: -1.57 (0.27), residues: 280 loop : -1.38 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 211 HIS 0.004 0.001 HIS G 225 PHE 0.009 0.001 PHE A 272 TYR 0.017 0.002 TYR E 226 ARG 0.004 0.000 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 426 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8544 (mmt) cc_final: 0.7812 (mmt) REVERT: A 135 SER cc_start: 0.9475 (t) cc_final: 0.9130 (p) REVERT: A 144 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8272 (tppt) REVERT: A 153 GLU cc_start: 0.8421 (pt0) cc_final: 0.8047 (pm20) REVERT: A 293 MET cc_start: 0.5153 (tmm) cc_final: 0.4757 (tmm) REVERT: B 70 MET cc_start: 0.6847 (mtm) cc_final: 0.6423 (mtt) REVERT: B 76 MET cc_start: 0.8379 (mmt) cc_final: 0.7585 (mmt) REVERT: B 104 ARG cc_start: 0.9203 (tpp80) cc_final: 0.8794 (tpp80) REVERT: B 133 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9091 (tt) REVERT: B 309 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7622 (mpp) REVERT: C 59 LYS cc_start: 0.8837 (ptpp) cc_final: 0.8328 (ttpt) REVERT: C 76 MET cc_start: 0.8460 (mmt) cc_final: 0.7503 (mmt) REVERT: C 112 GLU cc_start: 0.8600 (tp30) cc_final: 0.8068 (tp30) REVERT: C 144 LYS cc_start: 0.7555 (tptp) cc_final: 0.7003 (tppt) REVERT: C 309 MET cc_start: 0.7932 (mpp) cc_final: 0.7356 (mpp) REVERT: D 57 PHE cc_start: 0.8668 (m-80) cc_final: 0.8187 (m-80) REVERT: D 76 MET cc_start: 0.8276 (mmt) cc_final: 0.7398 (mmt) REVERT: D 123 ASP cc_start: 0.8374 (t0) cc_final: 0.8017 (m-30) REVERT: D 144 LYS cc_start: 0.7885 (tppt) cc_final: 0.7169 (tppt) REVERT: D 183 ASN cc_start: 0.9343 (t0) cc_final: 0.9118 (t0) REVERT: D 287 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8177 (mpt180) REVERT: D 309 MET cc_start: 0.8034 (mpp) cc_final: 0.7690 (mpp) REVERT: E 1 MET cc_start: 0.4712 (mmp) cc_final: 0.4004 (mpp) REVERT: E 56 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8312 (tm-30) REVERT: E 76 MET cc_start: 0.8355 (mmt) cc_final: 0.7681 (mmt) REVERT: E 95 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8571 (mm110) REVERT: E 122 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8664 (mm-40) REVERT: E 142 GLN cc_start: 0.8901 (mm110) cc_final: 0.8592 (mp10) REVERT: E 144 LYS cc_start: 0.7850 (tppt) cc_final: 0.7047 (tppt) REVERT: E 195 LYS cc_start: 0.9280 (ptpt) cc_final: 0.8918 (mtmt) REVERT: E 287 ARG cc_start: 0.9000 (ttp-170) cc_final: 0.8391 (mmt180) REVERT: E 309 MET cc_start: 0.7963 (mpp) cc_final: 0.7260 (mpp) REVERT: F 76 MET cc_start: 0.8472 (mmt) cc_final: 0.7497 (mmt) REVERT: F 82 MET cc_start: 0.7543 (tpt) cc_final: 0.7154 (tpt) REVERT: F 104 ARG cc_start: 0.8956 (tpp80) cc_final: 0.8711 (tpp80) REVERT: F 144 LYS cc_start: 0.8026 (tppt) cc_final: 0.7502 (tppt) REVERT: F 153 GLU cc_start: 0.8381 (pt0) cc_final: 0.7843 (pm20) REVERT: G 9 TYR cc_start: 0.7810 (p90) cc_final: 0.7451 (p90) REVERT: G 56 GLN cc_start: 0.8831 (tp40) cc_final: 0.8335 (tp40) REVERT: G 57 PHE cc_start: 0.8577 (m-10) cc_final: 0.8039 (m-80) REVERT: G 66 ASN cc_start: 0.8579 (p0) cc_final: 0.8371 (p0) REVERT: G 76 MET cc_start: 0.8377 (mmt) cc_final: 0.7676 (mmt) REVERT: G 82 MET cc_start: 0.7352 (tpt) cc_final: 0.6973 (tpt) REVERT: G 92 LYS cc_start: 0.8259 (tppt) cc_final: 0.7871 (tmtt) REVERT: G 112 GLU cc_start: 0.8824 (tp30) cc_final: 0.8281 (tp30) REVERT: G 144 LYS cc_start: 0.7747 (tppt) cc_final: 0.7263 (tppt) REVERT: G 195 LYS cc_start: 0.9197 (ptpp) cc_final: 0.8901 (mtmt) REVERT: G 309 MET cc_start: 0.7763 (mpp) cc_final: 0.7544 (mpp) REVERT: U 57 PHE cc_start: 0.8831 (m-80) cc_final: 0.8242 (m-80) REVERT: U 66 ASN cc_start: 0.7404 (t0) cc_final: 0.6091 (p0) REVERT: U 76 MET cc_start: 0.8349 (mmt) cc_final: 0.7438 (mmt) REVERT: U 104 ARG cc_start: 0.9187 (tpp80) cc_final: 0.8681 (tpp80) REVERT: U 144 LYS cc_start: 0.8117 (tppt) cc_final: 0.7381 (tppt) REVERT: U 183 ASN cc_start: 0.8973 (t0) cc_final: 0.8653 (t0) REVERT: U 287 ARG cc_start: 0.7819 (mmt90) cc_final: 0.7507 (mmt90) REVERT: U 309 MET cc_start: 0.7995 (mpp) cc_final: 0.7642 (mpp) outliers start: 86 outliers final: 74 residues processed: 466 average time/residue: 0.3255 time to fit residues: 227.7371 Evaluate side-chains 487 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 411 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 276 MET Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 71 ASN ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN G 212 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20800 Z= 0.166 Angle : 0.553 9.663 28088 Z= 0.279 Chirality : 0.040 0.197 3136 Planarity : 0.003 0.039 3560 Dihedral : 3.995 31.531 2688 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.26 % Allowed : 20.69 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2488 helix: 1.37 (0.18), residues: 824 sheet: -1.86 (0.27), residues: 296 loop : -1.31 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 211 HIS 0.002 0.000 HIS G 225 PHE 0.020 0.001 PHE E 272 TYR 0.013 0.001 TYR F 61 ARG 0.004 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 434 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 SER cc_start: 0.9453 (t) cc_final: 0.9094 (p) REVERT: A 144 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8229 (tppt) REVERT: A 153 GLU cc_start: 0.8271 (pt0) cc_final: 0.8005 (pm20) REVERT: A 293 MET cc_start: 0.5054 (tmm) cc_final: 0.4674 (tmm) REVERT: A 309 MET cc_start: 0.7612 (mpp) cc_final: 0.6908 (mpp) REVERT: B 22 PHE cc_start: 0.8290 (m-80) cc_final: 0.7948 (m-80) REVERT: B 70 MET cc_start: 0.6819 (mtm) cc_final: 0.6370 (mtt) REVERT: B 76 MET cc_start: 0.8304 (mmt) cc_final: 0.7494 (mmt) REVERT: B 104 ARG cc_start: 0.9254 (tpp80) cc_final: 0.8833 (tpp80) REVERT: B 133 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9054 (tt) REVERT: B 287 ARG cc_start: 0.8234 (mpt180) cc_final: 0.7862 (mpt180) REVERT: B 309 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: C 59 LYS cc_start: 0.8815 (ptpp) cc_final: 0.8328 (ttpt) REVERT: C 76 MET cc_start: 0.8431 (mmt) cc_final: 0.7492 (mmt) REVERT: C 112 GLU cc_start: 0.8687 (tp30) cc_final: 0.8008 (tp30) REVERT: C 144 LYS cc_start: 0.7506 (tptp) cc_final: 0.6952 (tppt) REVERT: C 309 MET cc_start: 0.7917 (mpp) cc_final: 0.7344 (mpp) REVERT: D 76 MET cc_start: 0.8315 (mmt) cc_final: 0.7452 (mmt) REVERT: D 123 ASP cc_start: 0.8341 (t0) cc_final: 0.8021 (m-30) REVERT: D 144 LYS cc_start: 0.7819 (tppt) cc_final: 0.7163 (tppt) REVERT: D 183 ASN cc_start: 0.9325 (t0) cc_final: 0.9094 (t0) REVERT: D 287 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8110 (mpt180) REVERT: D 293 MET cc_start: 0.4867 (ptp) cc_final: 0.2933 (ptm) REVERT: D 309 MET cc_start: 0.7948 (mpp) cc_final: 0.7608 (mpp) REVERT: E 1 MET cc_start: 0.4687 (mmp) cc_final: 0.4016 (mpp) REVERT: E 22 PHE cc_start: 0.8170 (m-80) cc_final: 0.7775 (m-80) REVERT: E 56 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8383 (tm-30) REVERT: E 76 MET cc_start: 0.8244 (mmt) cc_final: 0.7987 (mmt) REVERT: E 122 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8863 (mm-40) REVERT: E 142 GLN cc_start: 0.8845 (mm110) cc_final: 0.8591 (mp10) REVERT: E 144 LYS cc_start: 0.7813 (tppt) cc_final: 0.7026 (tppt) REVERT: E 172 LEU cc_start: 0.9370 (mt) cc_final: 0.8661 (tp) REVERT: E 195 LYS cc_start: 0.9253 (ptpt) cc_final: 0.8910 (mtmt) REVERT: E 287 ARG cc_start: 0.8993 (ttp-170) cc_final: 0.8342 (mmt180) REVERT: E 309 MET cc_start: 0.7918 (mpp) cc_final: 0.7618 (mpp) REVERT: F 76 MET cc_start: 0.8405 (mmt) cc_final: 0.7437 (mmt) REVERT: F 82 MET cc_start: 0.7477 (tpt) cc_final: 0.7099 (tpt) REVERT: F 104 ARG cc_start: 0.8986 (tpp80) cc_final: 0.8751 (tpp80) REVERT: F 144 LYS cc_start: 0.7993 (tppt) cc_final: 0.7483 (tppt) REVERT: F 309 MET cc_start: 0.7581 (mpp) cc_final: 0.7083 (mpp) REVERT: G 56 GLN cc_start: 0.8813 (tp40) cc_final: 0.8370 (tp40) REVERT: G 57 PHE cc_start: 0.8538 (m-10) cc_final: 0.7710 (m-80) REVERT: G 66 ASN cc_start: 0.8554 (p0) cc_final: 0.8344 (p0) REVERT: G 76 MET cc_start: 0.8298 (mmt) cc_final: 0.7557 (mmt) REVERT: G 82 MET cc_start: 0.7260 (tpt) cc_final: 0.6882 (tpt) REVERT: G 92 LYS cc_start: 0.8372 (tppt) cc_final: 0.7922 (tmtt) REVERT: G 144 LYS cc_start: 0.7719 (tppt) cc_final: 0.7250 (tppt) REVERT: G 195 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8842 (mtmt) REVERT: G 212 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8424 (tm130) REVERT: G 309 MET cc_start: 0.7727 (mpp) cc_final: 0.7490 (mpp) REVERT: U 57 PHE cc_start: 0.8760 (m-80) cc_final: 0.8157 (m-80) REVERT: U 66 ASN cc_start: 0.6868 (t0) cc_final: 0.6487 (t0) REVERT: U 76 MET cc_start: 0.8290 (mmt) cc_final: 0.7404 (mmt) REVERT: U 104 ARG cc_start: 0.9216 (tpp80) cc_final: 0.8715 (tpp80) REVERT: U 144 LYS cc_start: 0.8117 (tppt) cc_final: 0.7392 (tppt) REVERT: U 183 ASN cc_start: 0.8913 (t0) cc_final: 0.8630 (t0) REVERT: U 287 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7445 (mmt90) REVERT: U 293 MET cc_start: 0.6304 (ptp) cc_final: 0.5897 (ptp) REVERT: U 309 MET cc_start: 0.7997 (mpp) cc_final: 0.7682 (mpp) outliers start: 74 outliers final: 67 residues processed: 467 average time/residue: 0.3426 time to fit residues: 243.5768 Evaluate side-chains 490 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 420 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 276 MET Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 71 ASN ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 214 ASN E 183 ASN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN G 212 GLN U 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20800 Z= 0.187 Angle : 0.567 9.941 28088 Z= 0.286 Chirality : 0.040 0.198 3136 Planarity : 0.003 0.036 3560 Dihedral : 3.959 29.166 2688 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.35 % Allowed : 20.77 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2488 helix: 1.40 (0.18), residues: 824 sheet: -1.58 (0.27), residues: 280 loop : -1.31 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 211 HIS 0.002 0.001 HIS G 225 PHE 0.018 0.001 PHE E 272 TYR 0.024 0.001 TYR F 44 ARG 0.004 0.000 ARG C 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 422 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8451 (mmt) cc_final: 0.7783 (mmt) REVERT: A 135 SER cc_start: 0.9468 (t) cc_final: 0.9125 (p) REVERT: A 144 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8231 (tppt) REVERT: A 153 GLU cc_start: 0.8303 (pt0) cc_final: 0.8003 (pm20) REVERT: A 293 MET cc_start: 0.5046 (tmm) cc_final: 0.4669 (tmm) REVERT: A 309 MET cc_start: 0.7625 (mpp) cc_final: 0.7006 (mpp) REVERT: B 70 MET cc_start: 0.6817 (mtm) cc_final: 0.6390 (mtt) REVERT: B 76 MET cc_start: 0.8302 (mmt) cc_final: 0.7482 (mmt) REVERT: B 104 ARG cc_start: 0.9238 (tpp80) cc_final: 0.8821 (tpp80) REVERT: B 133 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9066 (tt) REVERT: B 287 ARG cc_start: 0.8250 (mpt180) cc_final: 0.7852 (mpt180) REVERT: B 309 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7556 (mpp) REVERT: C 59 LYS cc_start: 0.8826 (ptpp) cc_final: 0.8346 (ttpt) REVERT: C 76 MET cc_start: 0.8437 (mmt) cc_final: 0.7550 (mmt) REVERT: C 112 GLU cc_start: 0.8689 (tp30) cc_final: 0.8081 (tp30) REVERT: C 144 LYS cc_start: 0.7504 (tptp) cc_final: 0.6956 (tppt) REVERT: C 309 MET cc_start: 0.7936 (mpp) cc_final: 0.7373 (mpp) REVERT: D 57 PHE cc_start: 0.8569 (m-80) cc_final: 0.8059 (m-80) REVERT: D 76 MET cc_start: 0.8316 (mmt) cc_final: 0.7959 (mpp) REVERT: D 112 GLU cc_start: 0.8676 (tp30) cc_final: 0.8304 (tp30) REVERT: D 123 ASP cc_start: 0.8350 (t0) cc_final: 0.8037 (m-30) REVERT: D 144 LYS cc_start: 0.7822 (tppt) cc_final: 0.7171 (tppt) REVERT: D 183 ASN cc_start: 0.9321 (t0) cc_final: 0.9096 (t0) REVERT: D 287 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8107 (mpt180) REVERT: D 309 MET cc_start: 0.7976 (mpp) cc_final: 0.7596 (mpp) REVERT: E 1 MET cc_start: 0.4705 (mmp) cc_final: 0.4047 (mpp) REVERT: E 22 PHE cc_start: 0.8194 (m-80) cc_final: 0.7825 (m-80) REVERT: E 56 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8378 (tm-30) REVERT: E 76 MET cc_start: 0.8219 (mmt) cc_final: 0.7988 (mmt) REVERT: E 122 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8852 (mm-40) REVERT: E 142 GLN cc_start: 0.8852 (mm110) cc_final: 0.8588 (mp10) REVERT: E 144 LYS cc_start: 0.7813 (tppt) cc_final: 0.7034 (tppt) REVERT: E 172 LEU cc_start: 0.9380 (mt) cc_final: 0.8663 (tp) REVERT: E 195 LYS cc_start: 0.9258 (ptpt) cc_final: 0.8916 (mtmt) REVERT: E 287 ARG cc_start: 0.8982 (ttp-170) cc_final: 0.8293 (mmt90) REVERT: F 76 MET cc_start: 0.8441 (mmt) cc_final: 0.7480 (mmt) REVERT: F 82 MET cc_start: 0.7479 (tpt) cc_final: 0.7098 (tpt) REVERT: F 104 ARG cc_start: 0.8992 (tpp80) cc_final: 0.8759 (tpp80) REVERT: F 144 LYS cc_start: 0.7997 (tppt) cc_final: 0.7490 (tppt) REVERT: F 309 MET cc_start: 0.7592 (mpp) cc_final: 0.7101 (mpp) REVERT: G 9 TYR cc_start: 0.7849 (p90) cc_final: 0.7519 (p90) REVERT: G 56 GLN cc_start: 0.8808 (tp40) cc_final: 0.8369 (tp40) REVERT: G 57 PHE cc_start: 0.8524 (m-10) cc_final: 0.7707 (m-80) REVERT: G 76 MET cc_start: 0.8320 (mmt) cc_final: 0.7573 (mmt) REVERT: G 82 MET cc_start: 0.7270 (tpt) cc_final: 0.6885 (tpt) REVERT: G 92 LYS cc_start: 0.8325 (tppt) cc_final: 0.7920 (tmtt) REVERT: G 144 LYS cc_start: 0.7717 (tppt) cc_final: 0.7254 (tppt) REVERT: G 195 LYS cc_start: 0.9160 (ptpp) cc_final: 0.8864 (mtmt) REVERT: G 212 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8463 (tm130) REVERT: G 309 MET cc_start: 0.7722 (mpp) cc_final: 0.7517 (mpp) REVERT: U 57 PHE cc_start: 0.8781 (m-80) cc_final: 0.8174 (m-80) REVERT: U 66 ASN cc_start: 0.6862 (t0) cc_final: 0.6504 (t0) REVERT: U 76 MET cc_start: 0.8267 (mmt) cc_final: 0.7397 (mmt) REVERT: U 104 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8747 (tpp80) REVERT: U 144 LYS cc_start: 0.8114 (tppt) cc_final: 0.7389 (tppt) REVERT: U 183 ASN cc_start: 0.8920 (t0) cc_final: 0.8658 (t0) REVERT: U 287 ARG cc_start: 0.7816 (mmt90) cc_final: 0.7457 (mmt90) REVERT: U 293 MET cc_start: 0.6312 (ptp) cc_final: 0.5911 (ptp) REVERT: U 309 MET cc_start: 0.8014 (mpp) cc_final: 0.7685 (mpp) outliers start: 76 outliers final: 68 residues processed: 458 average time/residue: 0.3205 time to fit residues: 222.5712 Evaluate side-chains 488 residues out of total 2272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 417 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 239 ASP Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain U residue 27 ILE Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 197 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 241 VAL Chi-restraints excluded: chain U residue 276 MET Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain U residue 303 LEU Chi-restraints excluded: chain U residue 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 54 optimal weight: 0.0670 chunk 197 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 202 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 71 ASN ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN G 66 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN U 160 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115356 restraints weight = 34950.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118915 restraints weight = 22203.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121273 restraints weight = 16938.528| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20800 Z= 0.147 Angle : 0.559 10.019 28088 Z= 0.282 Chirality : 0.040 0.194 3136 Planarity : 0.003 0.038 3560 Dihedral : 3.874 25.568 2688 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.99 % Allowed : 21.21 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2488 helix: 1.51 (0.18), residues: 824 sheet: -1.82 (0.26), residues: 296 loop : -1.20 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 211 HIS 0.002 0.000 HIS C 201 PHE 0.019 0.001 PHE E 272 TYR 0.012 0.001 TYR F 61 ARG 0.004 0.000 ARG C 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4684.94 seconds wall clock time: 84 minutes 54.55 seconds (5094.55 seconds total)