Starting phenix.real_space_refine on Thu Sep 18 13:28:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bkj_9406/09_2025/5bkj_9406.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkj_9406/09_2025/5bkj_9406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5bkj_9406/09_2025/5bkj_9406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkj_9406/09_2025/5bkj_9406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5bkj_9406/09_2025/5bkj_9406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkj_9406/09_2025/5bkj_9406.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 68 5.16 5 C 10692 2.51 5 N 2897 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16939 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' K': 2, 'PGW': 1, 'YQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 3.25, per 1000 atoms: 0.19 Number of scatterers: 16939 At special positions: 0 Unit cell: (150.7, 150.7, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 68 16.00 P 4 15.00 O 3276 8.00 N 2897 7.00 C 10692 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: 1.43 Conformation dependent library (CDL) restraints added in 725.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 48.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.534A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 105 removed outlier: 3.758A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.830A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.597A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.634A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU D 171 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 230 through 240 removed outlier: 3.636A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.635A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.624A pdb=" N THR F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.770A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU H 171 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.635A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR H 289 " --> pdb=" O ILE H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 105 removed outlier: 3.759A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.831A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.572A pdb=" N PHE C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.973A pdb=" N ALA E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 105 removed outlier: 3.759A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.831A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.618A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 105 removed outlier: 3.758A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.830A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.663A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 325 through 334 removed outlier: 3.736A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR G 333 " --> pdb=" O ARG G 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 3.589A pdb=" N ASN A 158 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.873A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.511A pdb=" N GLY F 295 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY H 295 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.590A pdb=" N ASN C 158 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.873A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.590A pdb=" N ASN E 158 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.872A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.589A pdb=" N ASN G 158 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.871A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) 744 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: 2.70 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4581 1.33 - 1.45: 2559 1.45 - 1.57: 9908 1.57 - 1.69: 4 1.69 - 1.80: 116 Bond restraints: 17168 Sorted by residual: bond pdb=" C01 YQ1 A 404 " pdb=" N01 YQ1 A 404 " ideal model delta sigma weight residual 1.524 1.468 0.056 2.00e-02 2.50e+03 7.77e+00 bond pdb=" O12 PGW C 401 " pdb=" P PGW C 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" O12 PGW G 401 " pdb=" P PGW G 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O12 PGW A 401 " pdb=" P PGW A 401 " ideal model delta sigma weight residual 1.636 1.691 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O12 PGW E 401 " pdb=" P PGW E 401 " ideal model delta sigma weight residual 1.636 1.690 -0.054 2.00e-02 2.50e+03 7.40e+00 ... (remaining 17163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 22436 1.87 - 3.74: 585 3.74 - 5.61: 121 5.61 - 7.47: 40 7.47 - 9.34: 4 Bond angle restraints: 23186 Sorted by residual: angle pdb=" CG1 ILE D 285 " pdb=" CB ILE D 285 " pdb=" CG2 ILE D 285 " ideal model delta sigma weight residual 110.70 120.04 -9.34 3.00e+00 1.11e-01 9.70e+00 angle pdb=" CG1 ILE F 285 " pdb=" CB ILE F 285 " pdb=" CG2 ILE F 285 " ideal model delta sigma weight residual 110.70 120.00 -9.30 3.00e+00 1.11e-01 9.60e+00 angle pdb=" CG1 ILE H 285 " pdb=" CB ILE H 285 " pdb=" CG2 ILE H 285 " ideal model delta sigma weight residual 110.70 119.99 -9.29 3.00e+00 1.11e-01 9.59e+00 angle pdb=" CG1 ILE B 285 " pdb=" CB ILE B 285 " pdb=" CG2 ILE B 285 " ideal model delta sigma weight residual 110.70 119.96 -9.26 3.00e+00 1.11e-01 9.54e+00 angle pdb=" N LYS H 274 " pdb=" CA LYS H 274 " pdb=" C LYS H 274 " ideal model delta sigma weight residual 110.80 117.00 -6.20 2.13e+00 2.20e-01 8.47e+00 ... (remaining 23181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 9888 24.59 - 49.18: 524 49.18 - 73.77: 44 73.77 - 98.35: 28 98.35 - 122.94: 4 Dihedral angle restraints: 10488 sinusoidal: 4336 harmonic: 6152 Sorted by residual: dihedral pdb=" C01 PGW C 401 " pdb=" C19 PGW C 401 " pdb=" O03 PGW C 401 " pdb=" O04 PGW C 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.94 -122.94 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C01 PGW E 401 " pdb=" C19 PGW E 401 " pdb=" O03 PGW E 401 " pdb=" O04 PGW E 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.93 -122.93 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C01 PGW A 401 " pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " pdb=" O04 PGW A 401 " ideal model delta sinusoidal sigma weight residual 9.00 131.89 -122.89 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 2655 0.152 - 0.304: 29 0.304 - 0.455: 0 0.455 - 0.607: 0 0.607 - 0.759: 4 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CB ILE F 285 " pdb=" CA ILE F 285 " pdb=" CG1 ILE F 285 " pdb=" CG2 ILE F 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CB ILE H 285 " pdb=" CA ILE H 285 " pdb=" CG1 ILE H 285 " pdb=" CG2 ILE H 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CB ILE D 285 " pdb=" CA ILE D 285 " pdb=" CG1 ILE D 285 " pdb=" CG2 ILE D 285 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 2685 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 252 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C VAL F 252 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL F 252 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN F 253 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 252 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C VAL B 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL B 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN B 253 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 252 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C VAL H 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL H 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN H 253 " 0.011 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5166 2.83 - 3.41: 16311 3.41 - 3.98: 30344 3.98 - 4.56: 41421 4.56 - 5.14: 65321 Nonbonded interactions: 158563 Sorted by model distance: nonbonded pdb=" NH1 ARG A 154 " pdb=" O HIS C 161 " model vdw 2.251 3.120 nonbonded pdb=" O HIS A 161 " pdb=" NH1 ARG G 154 " model vdw 2.258 3.120 nonbonded pdb=" NH1 ARG C 154 " pdb=" O HIS E 161 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG E 154 " pdb=" O HIS G 161 " model vdw 2.283 3.120 nonbonded pdb=" O PHE A 75 " pdb=" OG1 THR A 78 " model vdw 2.304 3.040 ... (remaining 158558 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' and resid 20 through 401) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.940 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.340 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.006 0.056 17168 Z= 0.264 Angle : 0.813 9.342 23186 Z= 0.452 Chirality : 0.061 0.759 2688 Planarity : 0.005 0.034 3000 Dihedral : 15.402 122.943 6536 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.09 % Allowed : 7.64 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.13), residues: 2140 helix: -2.86 (0.11), residues: 980 sheet: -0.60 (0.25), residues: 356 loop : -3.04 (0.16), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 154 TYR 0.015 0.002 TYR C 51 PHE 0.007 0.001 PHE C 40 TRP 0.006 0.001 TRP G 123 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00584 (17168) covalent geometry : angle 0.81314 (23186) hydrogen bonds : bond 0.20029 ( 744) hydrogen bonds : angle 7.07524 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 519 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8109 (m-80) cc_final: 0.7310 (m-80) REVERT: A 82 LEU cc_start: 0.9295 (mt) cc_final: 0.8799 (mp) REVERT: A 105 LYS cc_start: 0.8850 (tttt) cc_final: 0.8597 (tttm) REVERT: A 174 ASN cc_start: 0.8910 (t0) cc_final: 0.8412 (t0) REVERT: A 319 LEU cc_start: 0.9182 (tp) cc_final: 0.8971 (tp) REVERT: B 174 ASN cc_start: 0.8532 (m110) cc_final: 0.8324 (m-40) REVERT: B 310 TYR cc_start: 0.7881 (t80) cc_final: 0.7501 (t80) REVERT: B 316 ASP cc_start: 0.8070 (m-30) cc_final: 0.7837 (m-30) REVERT: D 310 TYR cc_start: 0.7899 (t80) cc_final: 0.7507 (t80) REVERT: D 333 TYR cc_start: 0.8638 (t80) cc_final: 0.8090 (t80) REVERT: F 310 TYR cc_start: 0.7710 (t80) cc_final: 0.7416 (t80) REVERT: F 333 TYR cc_start: 0.8559 (t80) cc_final: 0.8074 (t80) REVERT: H 310 TYR cc_start: 0.7671 (t80) cc_final: 0.7455 (t80) REVERT: H 333 TYR cc_start: 0.8557 (t80) cc_final: 0.8076 (t80) REVERT: C 82 LEU cc_start: 0.9220 (mt) cc_final: 0.8754 (mp) REVERT: C 102 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 105 LYS cc_start: 0.8836 (tttt) cc_final: 0.8598 (tttm) REVERT: C 174 ASN cc_start: 0.8920 (t0) cc_final: 0.8428 (t0) REVERT: C 305 ASP cc_start: 0.7778 (t0) cc_final: 0.7568 (t70) REVERT: E 33 TYR cc_start: 0.8685 (t80) cc_final: 0.8278 (t80) REVERT: E 96 GLU cc_start: 0.7580 (tt0) cc_final: 0.7356 (tt0) REVERT: E 105 LYS cc_start: 0.8835 (tttt) cc_final: 0.8564 (tttm) REVERT: E 174 ASN cc_start: 0.8898 (t0) cc_final: 0.8418 (t0) REVERT: E 305 ASP cc_start: 0.7785 (t0) cc_final: 0.7530 (t70) REVERT: E 319 LEU cc_start: 0.9035 (tp) cc_final: 0.8823 (tp) REVERT: G 105 LYS cc_start: 0.8835 (tttt) cc_final: 0.8570 (tttm) REVERT: G 174 ASN cc_start: 0.8924 (t0) cc_final: 0.8420 (t0) outliers start: 20 outliers final: 0 residues processed: 527 average time/residue: 0.1606 time to fit residues: 120.1153 Evaluate side-chains 369 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 HIS B 332 ASN D 286 HIS H 286 HIS H 332 ASN C 219 GLN E 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.142392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110181 restraints weight = 21533.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113144 restraints weight = 13975.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.115051 restraints weight = 10365.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.116587 restraints weight = 8469.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117289 restraints weight = 7313.394| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17168 Z= 0.128 Angle : 0.501 5.338 23186 Z= 0.268 Chirality : 0.047 0.202 2688 Planarity : 0.004 0.046 3000 Dihedral : 9.121 74.027 2540 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.86 % Allowed : 13.43 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.16), residues: 2140 helix: -1.01 (0.15), residues: 992 sheet: -0.16 (0.26), residues: 356 loop : -2.69 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 241 TYR 0.018 0.001 TYR A 33 PHE 0.011 0.001 PHE F 251 TRP 0.003 0.000 TRP C 123 HIS 0.008 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00295 (17168) covalent geometry : angle 0.50102 (23186) hydrogen bonds : bond 0.03547 ( 744) hydrogen bonds : angle 4.81196 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 392 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8281 (m-80) cc_final: 0.7441 (m-80) REVERT: A 105 LYS cc_start: 0.8696 (tttt) cc_final: 0.8483 (tttm) REVERT: A 174 ASN cc_start: 0.8979 (t0) cc_final: 0.8384 (t0) REVERT: A 319 LEU cc_start: 0.9044 (tp) cc_final: 0.8831 (tp) REVERT: B 310 TYR cc_start: 0.8069 (t80) cc_final: 0.7838 (t80) REVERT: B 333 TYR cc_start: 0.8711 (t80) cc_final: 0.8213 (t80) REVERT: D 200 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8500 (tttt) REVERT: F 333 TYR cc_start: 0.8544 (t80) cc_final: 0.8187 (t80) REVERT: H 333 TYR cc_start: 0.8603 (t80) cc_final: 0.8180 (t80) REVERT: C 82 LEU cc_start: 0.9187 (mt) cc_final: 0.8787 (mp) REVERT: C 174 ASN cc_start: 0.8999 (t0) cc_final: 0.8426 (t0) REVERT: C 210 GLU cc_start: 0.7716 (tt0) cc_final: 0.7507 (tt0) REVERT: E 82 LEU cc_start: 0.9152 (mt) cc_final: 0.8780 (mp) REVERT: E 105 LYS cc_start: 0.8712 (tttt) cc_final: 0.8503 (tttm) REVERT: E 174 ASN cc_start: 0.8992 (t0) cc_final: 0.8414 (t0) REVERT: E 247 TYR cc_start: 0.8685 (m-80) cc_final: 0.8455 (m-80) REVERT: G 82 LEU cc_start: 0.9146 (mt) cc_final: 0.8790 (mp) REVERT: G 105 LYS cc_start: 0.8715 (tttt) cc_final: 0.8506 (tttm) REVERT: G 174 ASN cc_start: 0.8993 (t0) cc_final: 0.8412 (t0) REVERT: G 210 GLU cc_start: 0.7713 (tt0) cc_final: 0.7497 (tt0) outliers start: 34 outliers final: 21 residues processed: 414 average time/residue: 0.1486 time to fit residues: 88.8033 Evaluate side-chains 399 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 378 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 308 ARG Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 187 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 332 ASN F 286 HIS C 39 HIS E 39 HIS G 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111329 restraints weight = 21877.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114628 restraints weight = 15204.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115335 restraints weight = 10263.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115673 restraints weight = 9039.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115836 restraints weight = 8507.198| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17168 Z= 0.151 Angle : 0.486 4.619 23186 Z= 0.258 Chirality : 0.047 0.149 2688 Planarity : 0.003 0.031 3000 Dihedral : 8.409 78.363 2540 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.40 % Allowed : 15.99 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.17), residues: 2140 helix: -0.22 (0.16), residues: 1008 sheet: 0.09 (0.27), residues: 356 loop : -2.44 (0.18), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 241 TYR 0.026 0.002 TYR E 33 PHE 0.008 0.001 PHE H 140 TRP 0.004 0.001 TRP A 123 HIS 0.009 0.001 HIS F 286 Details of bonding type rmsd covalent geometry : bond 0.00362 (17168) covalent geometry : angle 0.48606 (23186) hydrogen bonds : bond 0.03513 ( 744) hydrogen bonds : angle 4.53341 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 385 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8343 (m-80) cc_final: 0.7456 (m-80) REVERT: A 105 LYS cc_start: 0.8737 (tttt) cc_final: 0.8410 (tttm) REVERT: A 174 ASN cc_start: 0.9001 (t0) cc_final: 0.8405 (t0) REVERT: A 210 GLU cc_start: 0.7744 (tt0) cc_final: 0.7471 (tt0) REVERT: A 237 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7653 (mmt90) REVERT: B 333 TYR cc_start: 0.8689 (t80) cc_final: 0.8262 (t80) REVERT: D 200 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8531 (tttt) REVERT: F 244 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7569 (p0) REVERT: F 333 TYR cc_start: 0.8673 (t80) cc_final: 0.8272 (t80) REVERT: H 333 TYR cc_start: 0.8616 (t80) cc_final: 0.8271 (t80) REVERT: C 65 TYR cc_start: 0.8388 (m-80) cc_final: 0.7550 (m-80) REVERT: C 82 LEU cc_start: 0.9238 (mt) cc_final: 0.8806 (mp) REVERT: C 102 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8236 (mm-30) REVERT: C 174 ASN cc_start: 0.9032 (t0) cc_final: 0.8430 (t0) REVERT: C 210 GLU cc_start: 0.7749 (tt0) cc_final: 0.7525 (tt0) REVERT: C 319 LEU cc_start: 0.9178 (tp) cc_final: 0.8952 (tp) REVERT: E 105 LYS cc_start: 0.8786 (tttt) cc_final: 0.8470 (tttm) REVERT: E 174 ASN cc_start: 0.9018 (t0) cc_final: 0.8417 (t0) REVERT: E 237 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7675 (mmt90) REVERT: G 65 TYR cc_start: 0.8415 (m-80) cc_final: 0.7552 (m-80) REVERT: G 82 LEU cc_start: 0.9219 (mt) cc_final: 0.8848 (mp) REVERT: G 102 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8182 (mm-30) REVERT: G 105 LYS cc_start: 0.8794 (tttt) cc_final: 0.8513 (tttm) REVERT: G 174 ASN cc_start: 0.9033 (t0) cc_final: 0.8440 (t0) REVERT: G 210 GLU cc_start: 0.7719 (tt0) cc_final: 0.7496 (tt0) REVERT: G 319 LEU cc_start: 0.9114 (tp) cc_final: 0.8893 (tp) outliers start: 44 outliers final: 32 residues processed: 413 average time/residue: 0.1454 time to fit residues: 88.2288 Evaluate side-chains 407 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 374 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 308 ARG Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 53 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 118 optimal weight: 0.0030 chunk 92 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111741 restraints weight = 21748.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112904 restraints weight = 19097.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114677 restraints weight = 14561.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115190 restraints weight = 11235.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115590 restraints weight = 9990.035| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17168 Z= 0.160 Angle : 0.479 4.446 23186 Z= 0.255 Chirality : 0.047 0.149 2688 Planarity : 0.003 0.025 3000 Dihedral : 8.175 87.302 2540 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.06 % Allowed : 18.56 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.17), residues: 2140 helix: 0.33 (0.16), residues: 992 sheet: 0.19 (0.28), residues: 356 loop : -2.29 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 241 TYR 0.024 0.001 TYR C 33 PHE 0.008 0.001 PHE G 97 TRP 0.004 0.001 TRP G 123 HIS 0.004 0.001 HIS F 286 Details of bonding type rmsd covalent geometry : bond 0.00388 (17168) covalent geometry : angle 0.47895 (23186) hydrogen bonds : bond 0.03292 ( 744) hydrogen bonds : angle 4.46903 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 378 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8327 (m-80) cc_final: 0.7433 (m-80) REVERT: A 82 LEU cc_start: 0.9264 (mt) cc_final: 0.8833 (mp) REVERT: A 100 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8461 (t0) REVERT: A 105 LYS cc_start: 0.8768 (tttt) cc_final: 0.8485 (tttm) REVERT: A 174 ASN cc_start: 0.9003 (t0) cc_final: 0.8593 (t0) REVERT: A 210 GLU cc_start: 0.7766 (tt0) cc_final: 0.7460 (tt0) REVERT: A 237 ARG cc_start: 0.7910 (mtt90) cc_final: 0.7636 (mmt90) REVERT: B 200 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8456 (tttt) REVERT: B 333 TYR cc_start: 0.8706 (t80) cc_final: 0.8351 (t80) REVERT: D 200 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8411 (tttt) REVERT: D 333 TYR cc_start: 0.8685 (t80) cc_final: 0.8303 (t80) REVERT: F 333 TYR cc_start: 0.8621 (t80) cc_final: 0.8213 (t80) REVERT: H 333 TYR cc_start: 0.8597 (t80) cc_final: 0.8299 (t80) REVERT: C 65 TYR cc_start: 0.8347 (m-80) cc_final: 0.7482 (m-80) REVERT: C 82 LEU cc_start: 0.9274 (mt) cc_final: 0.8836 (mp) REVERT: C 100 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8509 (t0) REVERT: C 174 ASN cc_start: 0.8989 (t0) cc_final: 0.8342 (t0) REVERT: C 210 GLU cc_start: 0.7766 (tt0) cc_final: 0.7520 (tt0) REVERT: E 65 TYR cc_start: 0.8391 (m-80) cc_final: 0.7564 (m-80) REVERT: E 105 LYS cc_start: 0.8772 (tttt) cc_final: 0.8465 (tttm) REVERT: E 174 ASN cc_start: 0.8987 (t0) cc_final: 0.8335 (t0) REVERT: E 237 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7641 (mmt90) REVERT: G 65 TYR cc_start: 0.8348 (m-80) cc_final: 0.7453 (m-80) REVERT: G 82 LEU cc_start: 0.9278 (mt) cc_final: 0.8850 (mp) REVERT: G 105 LYS cc_start: 0.8771 (tttt) cc_final: 0.8471 (tttm) REVERT: G 174 ASN cc_start: 0.8985 (t0) cc_final: 0.8551 (t0) REVERT: G 210 GLU cc_start: 0.7741 (tt0) cc_final: 0.7499 (tt0) REVERT: G 247 TYR cc_start: 0.8792 (m-80) cc_final: 0.8532 (m-80) outliers start: 56 outliers final: 43 residues processed: 412 average time/residue: 0.1401 time to fit residues: 85.9432 Evaluate side-chains 409 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 74 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112177 restraints weight = 21510.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113223 restraints weight = 18615.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115433 restraints weight = 14024.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115577 restraints weight = 11106.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115958 restraints weight = 10130.927| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17168 Z= 0.140 Angle : 0.463 4.753 23186 Z= 0.246 Chirality : 0.047 0.148 2688 Planarity : 0.003 0.030 3000 Dihedral : 7.855 89.625 2540 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.17 % Allowed : 19.71 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.18), residues: 2140 helix: 0.69 (0.17), residues: 996 sheet: 0.39 (0.28), residues: 352 loop : -2.10 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 237 TYR 0.026 0.001 TYR E 33 PHE 0.008 0.001 PHE F 251 TRP 0.003 0.001 TRP C 46 HIS 0.002 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00339 (17168) covalent geometry : angle 0.46265 (23186) hydrogen bonds : bond 0.03080 ( 744) hydrogen bonds : angle 4.38256 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 374 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8224 (m-80) cc_final: 0.7334 (m-80) REVERT: A 82 LEU cc_start: 0.9267 (mt) cc_final: 0.8828 (mp) REVERT: A 100 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8489 (t0) REVERT: A 105 LYS cc_start: 0.8749 (tttt) cc_final: 0.8508 (tttm) REVERT: A 174 ASN cc_start: 0.8935 (t0) cc_final: 0.8566 (t0) REVERT: A 200 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8557 (tttt) REVERT: A 210 GLU cc_start: 0.7663 (tt0) cc_final: 0.7371 (tt0) REVERT: A 237 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7638 (mmt90) REVERT: B 200 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8452 (tttt) REVERT: B 333 TYR cc_start: 0.8703 (t80) cc_final: 0.8417 (t80) REVERT: D 200 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8454 (tttt) REVERT: D 332 ASN cc_start: 0.7553 (m110) cc_final: 0.6954 (m110) REVERT: D 333 TYR cc_start: 0.8670 (t80) cc_final: 0.8344 (t80) REVERT: F 332 ASN cc_start: 0.7941 (m-40) cc_final: 0.7621 (m-40) REVERT: F 333 TYR cc_start: 0.8655 (t80) cc_final: 0.8361 (t80) REVERT: H 333 TYR cc_start: 0.8599 (t80) cc_final: 0.8361 (t80) REVERT: C 65 TYR cc_start: 0.8220 (m-80) cc_final: 0.7374 (m-80) REVERT: C 82 LEU cc_start: 0.9280 (mt) cc_final: 0.8826 (mp) REVERT: C 100 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8542 (t0) REVERT: C 174 ASN cc_start: 0.8946 (t0) cc_final: 0.8577 (t0) REVERT: C 200 LYS cc_start: 0.8835 (ttpt) cc_final: 0.8578 (tttt) REVERT: C 210 GLU cc_start: 0.7674 (tt0) cc_final: 0.7444 (tt0) REVERT: E 65 TYR cc_start: 0.8214 (m-80) cc_final: 0.7351 (m-80) REVERT: E 105 LYS cc_start: 0.8706 (tttt) cc_final: 0.8476 (tttm) REVERT: E 174 ASN cc_start: 0.8956 (t0) cc_final: 0.8567 (t0) REVERT: E 200 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8566 (tttt) REVERT: G 65 TYR cc_start: 0.8223 (m-80) cc_final: 0.7376 (m-80) REVERT: G 82 LEU cc_start: 0.9310 (mt) cc_final: 0.8861 (mp) REVERT: G 105 LYS cc_start: 0.8706 (tttt) cc_final: 0.8483 (tttm) REVERT: G 174 ASN cc_start: 0.8964 (t0) cc_final: 0.8566 (t0) REVERT: G 210 GLU cc_start: 0.7640 (tt0) cc_final: 0.7406 (tt0) REVERT: G 247 TYR cc_start: 0.8802 (m-80) cc_final: 0.8556 (m-80) outliers start: 58 outliers final: 48 residues processed: 408 average time/residue: 0.1350 time to fit residues: 82.8764 Evaluate side-chains 413 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 363 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.143410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113695 restraints weight = 21435.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115547 restraints weight = 17093.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117008 restraints weight = 12138.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.117360 restraints weight = 10344.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117713 restraints weight = 9481.579| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17168 Z= 0.101 Angle : 0.442 4.463 23186 Z= 0.235 Chirality : 0.046 0.145 2688 Planarity : 0.003 0.039 3000 Dihedral : 7.501 87.559 2540 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.89 % Allowed : 20.36 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.18), residues: 2140 helix: 1.09 (0.17), residues: 972 sheet: 0.45 (0.28), residues: 352 loop : -1.89 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.025 0.001 TYR C 33 PHE 0.005 0.001 PHE F 251 TRP 0.003 0.000 TRP G 46 HIS 0.001 0.000 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00239 (17168) covalent geometry : angle 0.44205 (23186) hydrogen bonds : bond 0.02665 ( 744) hydrogen bonds : angle 4.24144 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 372 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8372 (m-80) cc_final: 0.7450 (m-80) REVERT: A 82 LEU cc_start: 0.9246 (mt) cc_final: 0.8819 (mp) REVERT: A 93 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7947 (mmm160) REVERT: A 100 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8506 (t0) REVERT: A 105 LYS cc_start: 0.8688 (tttt) cc_final: 0.8397 (tttm) REVERT: A 111 ASP cc_start: 0.7445 (m-30) cc_final: 0.7150 (m-30) REVERT: A 174 ASN cc_start: 0.8994 (t0) cc_final: 0.8532 (t0) REVERT: A 200 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8498 (tttt) REVERT: A 210 GLU cc_start: 0.7763 (tt0) cc_final: 0.7441 (tt0) REVERT: A 237 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7624 (mmt90) REVERT: A 247 TYR cc_start: 0.8670 (m-80) cc_final: 0.8417 (m-80) REVERT: B 200 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8433 (tttt) REVERT: B 333 TYR cc_start: 0.8576 (t80) cc_final: 0.8264 (t80) REVERT: D 132 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7474 (ttm170) REVERT: D 200 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8420 (tttt) REVERT: D 247 TYR cc_start: 0.8547 (m-80) cc_final: 0.8236 (m-80) REVERT: D 333 TYR cc_start: 0.8575 (t80) cc_final: 0.8258 (t80) REVERT: F 333 TYR cc_start: 0.8564 (t80) cc_final: 0.8321 (t80) REVERT: H 333 TYR cc_start: 0.8551 (t80) cc_final: 0.8305 (t80) REVERT: C 65 TYR cc_start: 0.8375 (m-80) cc_final: 0.7494 (m-80) REVERT: C 82 LEU cc_start: 0.9258 (mt) cc_final: 0.8821 (mp) REVERT: C 100 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8548 (t0) REVERT: C 174 ASN cc_start: 0.9011 (t0) cc_final: 0.8550 (t0) REVERT: C 200 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8504 (tttt) REVERT: C 210 GLU cc_start: 0.7747 (tt0) cc_final: 0.7466 (tt0) REVERT: E 65 TYR cc_start: 0.8327 (m-80) cc_final: 0.7461 (m-80) REVERT: E 82 LEU cc_start: 0.9242 (mt) cc_final: 0.8818 (mp) REVERT: E 105 LYS cc_start: 0.8662 (tttt) cc_final: 0.8390 (tttm) REVERT: E 174 ASN cc_start: 0.9014 (t0) cc_final: 0.8528 (t0) REVERT: E 200 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8503 (tttt) REVERT: E 237 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7633 (mmt90) REVERT: E 247 TYR cc_start: 0.8741 (m-80) cc_final: 0.8481 (m-80) REVERT: G 65 TYR cc_start: 0.8366 (m-80) cc_final: 0.7491 (m-80) REVERT: G 82 LEU cc_start: 0.9296 (mt) cc_final: 0.8864 (mp) REVERT: G 104 MET cc_start: 0.8251 (ttt) cc_final: 0.7847 (ttp) REVERT: G 105 LYS cc_start: 0.8654 (tttt) cc_final: 0.8367 (tttm) REVERT: G 174 ASN cc_start: 0.9016 (t0) cc_final: 0.8526 (t0) REVERT: G 210 GLU cc_start: 0.7717 (tt0) cc_final: 0.7429 (tt0) REVERT: G 247 TYR cc_start: 0.8739 (m-80) cc_final: 0.8418 (m-80) outliers start: 53 outliers final: 45 residues processed: 400 average time/residue: 0.1346 time to fit residues: 79.8878 Evaluate side-chains 407 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 360 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 159 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.142455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112878 restraints weight = 21488.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113992 restraints weight = 18066.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115700 restraints weight = 13383.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.115944 restraints weight = 11386.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116356 restraints weight = 10213.145| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17168 Z= 0.135 Angle : 0.466 4.551 23186 Z= 0.246 Chirality : 0.047 0.147 2688 Planarity : 0.003 0.038 3000 Dihedral : 7.382 83.735 2540 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.28 % Allowed : 20.69 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.18), residues: 2140 helix: 1.21 (0.17), residues: 972 sheet: 0.49 (0.28), residues: 352 loop : -1.86 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 237 TYR 0.025 0.001 TYR G 33 PHE 0.006 0.001 PHE G 75 TRP 0.004 0.001 TRP C 46 HIS 0.002 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00327 (17168) covalent geometry : angle 0.46576 (23186) hydrogen bonds : bond 0.02940 ( 744) hydrogen bonds : angle 4.25810 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 371 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8358 (m-80) cc_final: 0.7430 (m-80) REVERT: A 82 LEU cc_start: 0.9255 (mt) cc_final: 0.8828 (mp) REVERT: A 93 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7963 (mmm160) REVERT: A 100 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8557 (t0) REVERT: A 105 LYS cc_start: 0.8687 (tttt) cc_final: 0.8406 (tttm) REVERT: A 111 ASP cc_start: 0.7445 (m-30) cc_final: 0.7159 (m-30) REVERT: A 174 ASN cc_start: 0.9009 (t0) cc_final: 0.8525 (t0) REVERT: A 200 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8502 (tttt) REVERT: A 210 GLU cc_start: 0.7740 (tt0) cc_final: 0.7440 (tt0) REVERT: A 237 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7642 (mmt90) REVERT: B 200 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8456 (tttt) REVERT: B 309 ASP cc_start: 0.7447 (m-30) cc_final: 0.6754 (p0) REVERT: B 333 TYR cc_start: 0.8580 (t80) cc_final: 0.8270 (t80) REVERT: D 132 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7434 (ttm170) REVERT: D 200 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8458 (tttt) REVERT: D 247 TYR cc_start: 0.8628 (m-80) cc_final: 0.8357 (m-80) REVERT: D 333 TYR cc_start: 0.8582 (t80) cc_final: 0.8261 (t80) REVERT: F 333 TYR cc_start: 0.8573 (t80) cc_final: 0.8350 (t80) REVERT: H 132 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7589 (ttp-170) REVERT: H 333 TYR cc_start: 0.8547 (t80) cc_final: 0.8308 (t80) REVERT: C 65 TYR cc_start: 0.8381 (m-80) cc_final: 0.7474 (m-80) REVERT: C 82 LEU cc_start: 0.9267 (mt) cc_final: 0.8830 (mp) REVERT: C 100 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8588 (t0) REVERT: C 104 MET cc_start: 0.8241 (ttt) cc_final: 0.7835 (ttp) REVERT: C 111 ASP cc_start: 0.7418 (m-30) cc_final: 0.7126 (m-30) REVERT: C 174 ASN cc_start: 0.9026 (t0) cc_final: 0.8541 (t0) REVERT: C 200 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8518 (tttt) REVERT: C 210 GLU cc_start: 0.7748 (tt0) cc_final: 0.7475 (tt0) REVERT: E 65 TYR cc_start: 0.8331 (m-80) cc_final: 0.7478 (m-80) REVERT: E 82 LEU cc_start: 0.9253 (mt) cc_final: 0.8831 (mp) REVERT: E 104 MET cc_start: 0.8269 (ttt) cc_final: 0.7864 (ttp) REVERT: E 105 LYS cc_start: 0.8665 (tttt) cc_final: 0.8407 (tttm) REVERT: E 111 ASP cc_start: 0.7448 (m-30) cc_final: 0.7148 (m-30) REVERT: E 174 ASN cc_start: 0.9017 (t0) cc_final: 0.8524 (t0) REVERT: E 200 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8503 (tttt) REVERT: E 237 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7629 (mmt90) REVERT: E 247 TYR cc_start: 0.8778 (m-80) cc_final: 0.8503 (m-80) REVERT: G 65 TYR cc_start: 0.8356 (m-80) cc_final: 0.7497 (m-80) REVERT: G 82 LEU cc_start: 0.9309 (mt) cc_final: 0.8873 (mp) REVERT: G 104 MET cc_start: 0.8260 (ttt) cc_final: 0.7862 (ttp) REVERT: G 105 LYS cc_start: 0.8651 (tttt) cc_final: 0.8381 (tttm) REVERT: G 111 ASP cc_start: 0.7416 (m-30) cc_final: 0.7118 (m-30) REVERT: G 174 ASN cc_start: 0.9019 (t0) cc_final: 0.8535 (t0) REVERT: G 210 GLU cc_start: 0.7717 (tt0) cc_final: 0.7455 (tt0) REVERT: G 237 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7338 (mmt90) REVERT: G 247 TYR cc_start: 0.8788 (m-80) cc_final: 0.8530 (m-80) outliers start: 60 outliers final: 49 residues processed: 410 average time/residue: 0.1341 time to fit residues: 82.1332 Evaluate side-chains 413 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 362 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 177 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 203 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 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 332 ASN C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.151177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122967 restraints weight = 21115.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125342 restraints weight = 14826.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126828 restraints weight = 10187.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127113 restraints weight = 8316.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127285 restraints weight = 7569.394| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17168 Z= 0.112 Angle : 0.467 7.063 23186 Z= 0.244 Chirality : 0.047 0.210 2688 Planarity : 0.003 0.029 3000 Dihedral : 7.187 79.426 2540 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.00 % Allowed : 21.34 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.18), residues: 2140 helix: 1.30 (0.17), residues: 972 sheet: 0.56 (0.29), residues: 352 loop : -1.82 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 237 TYR 0.025 0.001 TYR A 33 PHE 0.005 0.001 PHE H 140 TRP 0.003 0.001 TRP A 46 HIS 0.001 0.000 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00270 (17168) covalent geometry : angle 0.46713 (23186) hydrogen bonds : bond 0.02754 ( 744) hydrogen bonds : angle 4.22993 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 370 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8424 (m-80) cc_final: 0.7479 (m-80) REVERT: A 82 LEU cc_start: 0.9237 (mt) cc_final: 0.9002 (mt) REVERT: A 93 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7987 (mmm160) REVERT: A 100 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8578 (t0) REVERT: A 104 MET cc_start: 0.8262 (ttt) cc_final: 0.7878 (ttp) REVERT: A 105 LYS cc_start: 0.8738 (tttt) cc_final: 0.8457 (tttm) REVERT: A 111 ASP cc_start: 0.7345 (m-30) cc_final: 0.7070 (m-30) REVERT: A 174 ASN cc_start: 0.8997 (t0) cc_final: 0.8347 (t0) REVERT: A 200 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8450 (tttt) REVERT: A 210 GLU cc_start: 0.7748 (tt0) cc_final: 0.7429 (tt0) REVERT: A 237 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7620 (mmt90) REVERT: A 247 TYR cc_start: 0.8703 (m-80) cc_final: 0.8402 (m-80) REVERT: B 200 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8440 (tttt) REVERT: B 309 ASP cc_start: 0.7447 (m-30) cc_final: 0.6790 (p0) REVERT: B 333 TYR cc_start: 0.8545 (t80) cc_final: 0.8240 (t80) REVERT: D 132 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7476 (ttm170) REVERT: D 200 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8450 (tttt) REVERT: D 247 TYR cc_start: 0.8643 (m-80) cc_final: 0.8390 (m-80) REVERT: D 309 ASP cc_start: 0.7447 (m-30) cc_final: 0.6772 (p0) REVERT: D 333 TYR cc_start: 0.8513 (t80) cc_final: 0.8212 (t80) REVERT: F 309 ASP cc_start: 0.7487 (m-30) cc_final: 0.6895 (p0) REVERT: F 332 ASN cc_start: 0.7769 (m-40) cc_final: 0.7352 (m110) REVERT: F 333 TYR cc_start: 0.8545 (t80) cc_final: 0.8296 (t80) REVERT: H 309 ASP cc_start: 0.7498 (m-30) cc_final: 0.6771 (p0) REVERT: H 333 TYR cc_start: 0.8504 (t80) cc_final: 0.8259 (t80) REVERT: C 65 TYR cc_start: 0.8459 (m-80) cc_final: 0.7551 (m-80) REVERT: C 82 LEU cc_start: 0.9247 (mt) cc_final: 0.8817 (mp) REVERT: C 100 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8584 (t0) REVERT: C 104 MET cc_start: 0.8230 (ttt) cc_final: 0.7826 (ttp) REVERT: C 111 ASP cc_start: 0.7319 (m-30) cc_final: 0.7040 (m-30) REVERT: C 174 ASN cc_start: 0.9014 (t0) cc_final: 0.8745 (t0) REVERT: C 200 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8470 (tttt) REVERT: C 210 GLU cc_start: 0.7750 (tt0) cc_final: 0.7464 (tt0) REVERT: E 65 TYR cc_start: 0.8320 (m-80) cc_final: 0.7460 (m-80) REVERT: E 82 LEU cc_start: 0.9235 (mt) cc_final: 0.8818 (mp) REVERT: E 104 MET cc_start: 0.8257 (ttt) cc_final: 0.7860 (ttp) REVERT: E 105 LYS cc_start: 0.8713 (tttt) cc_final: 0.8451 (tttm) REVERT: E 111 ASP cc_start: 0.7322 (m-30) cc_final: 0.7034 (m-30) REVERT: E 174 ASN cc_start: 0.8994 (t0) cc_final: 0.8733 (t0) REVERT: E 200 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8470 (tttt) REVERT: E 237 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7614 (mmt90) REVERT: E 247 TYR cc_start: 0.8764 (m-80) cc_final: 0.8494 (m-80) REVERT: G 65 TYR cc_start: 0.8343 (m-80) cc_final: 0.7427 (m-80) REVERT: G 82 LEU cc_start: 0.9308 (mt) cc_final: 0.8882 (mp) REVERT: G 104 MET cc_start: 0.8265 (ttt) cc_final: 0.7862 (ttp) REVERT: G 105 LYS cc_start: 0.8703 (tttt) cc_final: 0.8436 (tttm) REVERT: G 111 ASP cc_start: 0.7332 (m-30) cc_final: 0.7036 (m-30) REVERT: G 174 ASN cc_start: 0.9005 (t0) cc_final: 0.8736 (t0) REVERT: G 210 GLU cc_start: 0.7728 (tt0) cc_final: 0.7444 (tt0) REVERT: G 237 ARG cc_start: 0.7601 (mtt-85) cc_final: 0.7296 (mmt90) REVERT: G 247 TYR cc_start: 0.8768 (m-80) cc_final: 0.8455 (m-80) outliers start: 55 outliers final: 45 residues processed: 404 average time/residue: 0.1311 time to fit residues: 79.2231 Evaluate side-chains 408 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 361 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 50 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN C 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.140231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110710 restraints weight = 21623.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.111758 restraints weight = 18497.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.112427 restraints weight = 14895.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113545 restraints weight = 12468.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.113718 restraints weight = 11059.864| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17168 Z= 0.173 Angle : 0.518 8.397 23186 Z= 0.269 Chirality : 0.049 0.221 2688 Planarity : 0.003 0.025 3000 Dihedral : 7.274 73.292 2540 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.73 % Allowed : 21.89 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.18), residues: 2140 helix: 1.31 (0.17), residues: 968 sheet: 0.49 (0.28), residues: 356 loop : -1.86 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 237 TYR 0.027 0.002 TYR A 33 PHE 0.008 0.001 PHE A 75 TRP 0.004 0.001 TRP A 46 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00424 (17168) covalent geometry : angle 0.51796 (23186) hydrogen bonds : bond 0.03352 ( 744) hydrogen bonds : angle 4.34316 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 383 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8254 (m-80) cc_final: 0.7377 (m-80) REVERT: A 100 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8544 (t0) REVERT: A 104 MET cc_start: 0.8337 (ttt) cc_final: 0.8015 (ttp) REVERT: A 105 LYS cc_start: 0.8734 (tttt) cc_final: 0.8496 (tttm) REVERT: A 111 ASP cc_start: 0.7260 (m-30) cc_final: 0.7001 (m-30) REVERT: A 174 ASN cc_start: 0.8953 (t0) cc_final: 0.8569 (t0) REVERT: A 200 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8483 (tttt) REVERT: A 237 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7625 (mmt90) REVERT: A 305 ASP cc_start: 0.7724 (t70) cc_final: 0.7517 (t0) REVERT: B 333 TYR cc_start: 0.8626 (t80) cc_final: 0.8319 (t80) REVERT: D 132 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7536 (mtm-85) REVERT: D 247 TYR cc_start: 0.8796 (m-80) cc_final: 0.8556 (m-80) REVERT: D 332 ASN cc_start: 0.7589 (m110) cc_final: 0.7305 (m110) REVERT: D 333 TYR cc_start: 0.8593 (t80) cc_final: 0.8298 (t80) REVERT: F 333 TYR cc_start: 0.8603 (t80) cc_final: 0.8364 (t80) REVERT: H 132 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7430 (ttm170) REVERT: H 333 TYR cc_start: 0.8589 (t80) cc_final: 0.8346 (t80) REVERT: C 65 TYR cc_start: 0.8279 (m-80) cc_final: 0.7360 (m-80) REVERT: C 100 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8549 (t0) REVERT: C 104 MET cc_start: 0.8273 (ttt) cc_final: 0.7928 (ttp) REVERT: C 111 ASP cc_start: 0.7220 (m-30) cc_final: 0.6956 (m-30) REVERT: C 174 ASN cc_start: 0.8978 (t0) cc_final: 0.8585 (t0) REVERT: C 200 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8495 (tttt) REVERT: C 210 GLU cc_start: 0.7615 (tt0) cc_final: 0.7397 (tt0) REVERT: E 65 TYR cc_start: 0.8160 (m-80) cc_final: 0.7313 (m-80) REVERT: E 104 MET cc_start: 0.8341 (ttt) cc_final: 0.7998 (ttp) REVERT: E 105 LYS cc_start: 0.8661 (tttt) cc_final: 0.8426 (tttm) REVERT: E 111 ASP cc_start: 0.7238 (m-30) cc_final: 0.6963 (m-30) REVERT: E 174 ASN cc_start: 0.8963 (t0) cc_final: 0.8572 (t0) REVERT: E 200 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8487 (tttt) REVERT: E 237 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7605 (mmt90) REVERT: G 65 TYR cc_start: 0.8217 (m-80) cc_final: 0.7320 (m-80) REVERT: G 104 MET cc_start: 0.8329 (ttt) cc_final: 0.7975 (ttp) REVERT: G 105 LYS cc_start: 0.8651 (tttt) cc_final: 0.8425 (tttm) REVERT: G 111 ASP cc_start: 0.7223 (m-30) cc_final: 0.6949 (m-30) REVERT: G 174 ASN cc_start: 0.8975 (t0) cc_final: 0.8578 (t0) REVERT: G 210 GLU cc_start: 0.7584 (tt0) cc_final: 0.7368 (tt0) outliers start: 50 outliers final: 45 residues processed: 415 average time/residue: 0.1345 time to fit residues: 83.9148 Evaluate side-chains 429 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 382 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.142898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.113640 restraints weight = 21305.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.116579 restraints weight = 16766.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117884 restraints weight = 11147.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117921 restraints weight = 9296.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118095 restraints weight = 8764.614| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17168 Z= 0.103 Angle : 0.474 7.761 23186 Z= 0.245 Chirality : 0.047 0.208 2688 Planarity : 0.002 0.025 3000 Dihedral : 6.973 66.601 2540 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.57 % Allowed : 22.38 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.18), residues: 2140 helix: 1.46 (0.17), residues: 972 sheet: 0.62 (0.29), residues: 352 loop : -1.78 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.028 0.001 TYR A 33 PHE 0.004 0.001 PHE A 75 TRP 0.003 0.001 TRP E 52 HIS 0.001 0.000 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00245 (17168) covalent geometry : angle 0.47394 (23186) hydrogen bonds : bond 0.02725 ( 744) hydrogen bonds : angle 4.22466 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 368 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8346 (m-80) cc_final: 0.7448 (m-80) REVERT: A 104 MET cc_start: 0.8282 (ttt) cc_final: 0.7886 (ttp) REVERT: A 105 LYS cc_start: 0.8732 (tttt) cc_final: 0.8448 (tttm) REVERT: A 111 ASP cc_start: 0.7401 (m-30) cc_final: 0.7106 (m-30) REVERT: A 174 ASN cc_start: 0.8994 (t0) cc_final: 0.8717 (t0) REVERT: A 200 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8400 (tttt) REVERT: A 237 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7623 (mmt90) REVERT: A 247 TYR cc_start: 0.8717 (m-80) cc_final: 0.8425 (m-80) REVERT: A 305 ASP cc_start: 0.7706 (t70) cc_final: 0.7452 (t70) REVERT: B 200 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8411 (tttt) REVERT: B 333 TYR cc_start: 0.8524 (t80) cc_final: 0.8246 (t80) REVERT: D 132 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7425 (ttm170) REVERT: D 247 TYR cc_start: 0.8695 (m-80) cc_final: 0.8467 (m-80) REVERT: D 333 TYR cc_start: 0.8524 (t80) cc_final: 0.8225 (t80) REVERT: F 200 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8159 (tttt) REVERT: F 333 TYR cc_start: 0.8522 (t80) cc_final: 0.8252 (t80) REVERT: H 333 TYR cc_start: 0.8508 (t80) cc_final: 0.8263 (t80) REVERT: C 65 TYR cc_start: 0.8429 (m-80) cc_final: 0.7494 (m-80) REVERT: C 93 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7669 (mmm160) REVERT: C 100 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8590 (t0) REVERT: C 104 MET cc_start: 0.8245 (ttt) cc_final: 0.7848 (ttp) REVERT: C 111 ASP cc_start: 0.7377 (m-30) cc_final: 0.7084 (m-30) REVERT: C 172 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8474 (mmtp) REVERT: C 174 ASN cc_start: 0.9018 (t0) cc_final: 0.8717 (t0) REVERT: C 200 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8398 (tttt) REVERT: C 210 GLU cc_start: 0.7730 (tt0) cc_final: 0.7449 (tt0) REVERT: E 65 TYR cc_start: 0.8291 (m-80) cc_final: 0.7429 (m-80) REVERT: E 82 LEU cc_start: 0.9241 (mt) cc_final: 0.9014 (mt) REVERT: E 104 MET cc_start: 0.8299 (ttt) cc_final: 0.7917 (ttp) REVERT: E 105 LYS cc_start: 0.8706 (tttt) cc_final: 0.8350 (tttm) REVERT: E 111 ASP cc_start: 0.7375 (m-30) cc_final: 0.7068 (m-30) REVERT: E 172 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8458 (mmtp) REVERT: E 174 ASN cc_start: 0.9007 (t0) cc_final: 0.8722 (t0) REVERT: E 200 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8408 (tttt) REVERT: E 237 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7616 (mmt90) REVERT: E 247 TYR cc_start: 0.8789 (m-80) cc_final: 0.8519 (m-80) REVERT: G 65 TYR cc_start: 0.8351 (m-80) cc_final: 0.7419 (m-80) REVERT: G 82 LEU cc_start: 0.9169 (mt) cc_final: 0.8798 (mp) REVERT: G 104 MET cc_start: 0.8282 (ttt) cc_final: 0.7884 (ttp) REVERT: G 105 LYS cc_start: 0.8698 (tttt) cc_final: 0.8434 (tttm) REVERT: G 111 ASP cc_start: 0.7372 (m-30) cc_final: 0.7083 (m-30) REVERT: G 174 ASN cc_start: 0.9010 (t0) cc_final: 0.8717 (t0) REVERT: G 210 GLU cc_start: 0.7710 (tt0) cc_final: 0.7425 (tt0) REVERT: G 247 TYR cc_start: 0.8787 (m-80) cc_final: 0.8556 (m-80) outliers start: 47 outliers final: 43 residues processed: 399 average time/residue: 0.1327 time to fit residues: 79.4741 Evaluate side-chains 412 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 368 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 147 optimal weight: 0.0010 chunk 187 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.142131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.112687 restraints weight = 21433.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115632 restraints weight = 16898.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116830 restraints weight = 11361.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.117094 restraints weight = 9181.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.117251 restraints weight = 8715.575| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17168 Z= 0.114 Angle : 0.482 7.970 23186 Z= 0.248 Chirality : 0.047 0.193 2688 Planarity : 0.002 0.030 3000 Dihedral : 6.801 64.421 2540 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.40 % Allowed : 23.14 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.18), residues: 2140 helix: 1.52 (0.17), residues: 972 sheet: 0.65 (0.29), residues: 352 loop : -1.75 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 237 TYR 0.027 0.001 TYR A 33 PHE 0.009 0.001 PHE A 75 TRP 0.004 0.001 TRP A 46 HIS 0.002 0.000 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00277 (17168) covalent geometry : angle 0.48188 (23186) hydrogen bonds : bond 0.02805 ( 744) hydrogen bonds : angle 4.18553 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.67 seconds wall clock time: 50 minutes 59.05 seconds (3059.05 seconds total)