Starting phenix.real_space_refine on Mon Apr 6 07:50:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bkj_9406/04_2026/5bkj_9406.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkj_9406/04_2026/5bkj_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_9406/04_2026/5bkj_9406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkj_9406/04_2026/5bkj_9406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5bkj_9406/04_2026/5bkj_9406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkj_9406/04_2026/5bkj_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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16939 Number of models: 1 Model: "" Number of chains: 16 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: "D" 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: "F" 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: "H" 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: "C" 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: "E" 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: "G" 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: "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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} 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} Time building chain proxies: 3.81, per 1000 atoms: 0.22 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: 1.57 Conformation dependent library (CDL) restraints added in 742.4 milliseconds 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: 0.45 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: 3.17 Time building geometry restraints manager: 2.05 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.930 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- 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 are 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: 0.8911 (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: 0.9219 (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: 0.1500 time to fit residues: 113.4964 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 : 0.567 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110181 restraints weight = 21533.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113142 restraints weight = 13975.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115185 restraints weight = 10367.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116432 restraints weight = 8434.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.117447 restraints weight = 7342.826| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 are 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 : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8370 (m-80) cc_final: 0.7521 (m-80) REVERT: A 105 LYS cc_start: 0.8679 (tttt) cc_final: 0.8417 (tttm) REVERT: A 174 ASN cc_start: 0.8990 (t0) cc_final: 0.8300 (t0) REVERT: B 310 TYR cc_start: 0.8135 (t80) cc_final: 0.7910 (t80) REVERT: B 333 TYR cc_start: 0.8652 (t80) cc_final: 0.8135 (t80) REVERT: D 200 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8480 (tttt) REVERT: F 333 TYR cc_start: 0.8476 (t80) cc_final: 0.8103 (t80) REVERT: H 333 TYR cc_start: 0.8559 (t80) cc_final: 0.8100 (t80) REVERT: C 82 LEU cc_start: 0.9148 (mt) cc_final: 0.8761 (mp) REVERT: C 105 LYS cc_start: 0.8699 (tttt) cc_final: 0.8469 (ttpp) REVERT: C 174 ASN cc_start: 0.9012 (t0) cc_final: 0.8344 (t0) REVERT: C 210 GLU cc_start: 0.7797 (tt0) cc_final: 0.7570 (tt0) REVERT: E 82 LEU cc_start: 0.9115 (mt) cc_final: 0.8751 (mp) REVERT: E 105 LYS cc_start: 0.8697 (tttt) cc_final: 0.8438 (tttm) REVERT: E 174 ASN cc_start: 0.9004 (t0) cc_final: 0.8332 (t0) REVERT: E 210 GLU cc_start: 0.7783 (tt0) cc_final: 0.7565 (tt0) REVERT: E 247 TYR cc_start: 0.8616 (m-80) cc_final: 0.8355 (m-80) REVERT: G 82 LEU cc_start: 0.9112 (mt) cc_final: 0.8765 (mp) REVERT: G 105 LYS cc_start: 0.8697 (tttt) cc_final: 0.8441 (tttm) REVERT: G 174 ASN cc_start: 0.9006 (t0) cc_final: 0.8327 (t0) REVERT: G 210 GLU cc_start: 0.7794 (tt0) cc_final: 0.7560 (tt0) outliers start: 34 outliers final: 21 residues processed: 414 average time/residue: 0.1440 time to fit residues: 86.1768 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 : 0.550 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.142087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110729 restraints weight = 21909.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113627 restraints weight = 17319.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114785 restraints weight = 11289.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115063 restraints weight = 9916.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115423 restraints weight = 9150.334| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2143 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= 0.152 Angle : 0.487 4.623 23186 Z= 0.259 Chirality : 0.047 0.148 2688 Planarity : 0.003 0.031 3000 Dihedral : 8.407 78.456 2540 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.46 % Allowed : 15.88 % Favored : 81.66 % 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 are not related in a simple way. whole: -1.46 (0.17), residues: 2140 helix: -0.23 (0.16), residues: 1008 sheet: 0.08 (0.27), residues: 356 loop : -2.44 (0.18), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 262 TYR 0.024 0.002 TYR E 33 PHE 0.008 0.001 PHE H 140 TRP 0.004 0.001 TRP A 123 HIS 0.010 0.001 HIS F 286 Details of bonding type rmsd covalent geometry : bond 0.00365 (17168) covalent geometry : angle 0.48726 (23186) hydrogen bonds : bond 0.03543 ( 744) hydrogen bonds : angle 4.54035 ( 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 432 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 387 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: 0.8426 (m-80) cc_final: 0.7526 (m-80) REVERT: A 105 LYS cc_start: 0.8722 (tttt) cc_final: 0.8354 (tttm) REVERT: A 174 ASN cc_start: 0.9018 (t0) cc_final: 0.8333 (t0) REVERT: A 237 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7673 (mmt90) REVERT: B 333 TYR cc_start: 0.8648 (t80) cc_final: 0.8220 (t80) REVERT: D 200 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8473 (tttt) REVERT: F 244 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7484 (p0) REVERT: F 333 TYR cc_start: 0.8641 (t80) cc_final: 0.8205 (t80) REVERT: H 333 TYR cc_start: 0.8585 (t80) cc_final: 0.8216 (t80) REVERT: C 65 TYR cc_start: 0.8467 (m-80) cc_final: 0.7629 (m-80) REVERT: C 82 LEU cc_start: 0.9213 (mt) cc_final: 0.8798 (mp) REVERT: C 102 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8323 (mm-30) REVERT: C 105 LYS cc_start: 0.8777 (tttt) cc_final: 0.8425 (tttm) REVERT: C 174 ASN cc_start: 0.9043 (t0) cc_final: 0.8351 (t0) REVERT: C 210 GLU cc_start: 0.7817 (tt0) cc_final: 0.7580 (tt0) REVERT: C 319 LEU cc_start: 0.9074 (tp) cc_final: 0.8864 (tp) REVERT: E 82 LEU cc_start: 0.9197 (mt) cc_final: 0.8833 (mp) REVERT: E 105 LYS cc_start: 0.8738 (tttt) cc_final: 0.8366 (tttm) REVERT: E 174 ASN cc_start: 0.9031 (t0) cc_final: 0.8342 (t0) REVERT: E 210 GLU cc_start: 0.7806 (tt0) cc_final: 0.7570 (tt0) REVERT: E 237 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7623 (mtt-85) REVERT: G 65 TYR cc_start: 0.8489 (m-80) cc_final: 0.7620 (m-80) REVERT: G 82 LEU cc_start: 0.9195 (mt) cc_final: 0.8833 (mp) REVERT: G 102 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8293 (mm-30) REVERT: G 105 LYS cc_start: 0.8772 (tttt) cc_final: 0.8429 (tttm) REVERT: G 174 ASN cc_start: 0.9047 (t0) cc_final: 0.8361 (t0) REVERT: G 210 GLU cc_start: 0.7795 (tt0) cc_final: 0.7557 (tt0) REVERT: G 319 LEU cc_start: 0.9009 (tp) cc_final: 0.8809 (tp) outliers start: 45 outliers final: 33 residues processed: 415 average time/residue: 0.1427 time to fit residues: 87.4027 Evaluate side-chains 411 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 377 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 35 THR 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: 4.9990 chunk 152 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 0.0470 chunk 92 optimal weight: 0.0270 chunk 172 optimal weight: 0.2980 chunk 211 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115756 restraints weight = 21483.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118169 restraints weight = 16729.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119726 restraints weight = 11461.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119880 restraints weight = 9727.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120230 restraints weight = 8970.475| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17168 Z= 0.079 Angle : 0.423 4.389 23186 Z= 0.226 Chirality : 0.045 0.142 2688 Planarity : 0.003 0.028 3000 Dihedral : 7.723 79.423 2540 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.80 % Allowed : 18.29 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2140 helix: 0.47 (0.17), residues: 992 sheet: 0.32 (0.28), residues: 352 loop : -2.30 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 241 TYR 0.022 0.001 TYR G 33 PHE 0.006 0.001 PHE C 75 TRP 0.002 0.000 TRP D 123 HIS 0.004 0.001 HIS F 286 Details of bonding type rmsd covalent geometry : bond 0.00171 (17168) covalent geometry : angle 0.42308 (23186) hydrogen bonds : bond 0.02444 ( 744) hydrogen bonds : angle 4.26720 ( 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 418 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 385 time to evaluate : 0.399 Fit side-chains REVERT: A 65 TYR cc_start: 0.8339 (m-80) cc_final: 0.7452 (m-80) REVERT: A 82 LEU cc_start: 0.9225 (mt) cc_final: 0.8808 (mp) REVERT: A 100 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8528 (t0) REVERT: A 105 LYS cc_start: 0.8763 (tttt) cc_final: 0.8471 (tttm) REVERT: A 174 ASN cc_start: 0.8982 (t0) cc_final: 0.8342 (t0) REVERT: A 210 GLU cc_start: 0.7724 (tt0) cc_final: 0.7411 (tt0) REVERT: A 237 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7548 (mmt90) REVERT: B 200 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8374 (tttt) REVERT: B 333 TYR cc_start: 0.8640 (t80) cc_final: 0.8276 (t80) REVERT: D 200 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8421 (tttt) REVERT: D 247 TYR cc_start: 0.8073 (m-80) cc_final: 0.7796 (m-80) REVERT: D 333 TYR cc_start: 0.8650 (t80) cc_final: 0.8226 (t80) REVERT: F 333 TYR cc_start: 0.8555 (t80) cc_final: 0.8190 (t80) REVERT: H 333 TYR cc_start: 0.8570 (t80) cc_final: 0.8318 (t80) REVERT: C 65 TYR cc_start: 0.8355 (m-80) cc_final: 0.7572 (m-80) REVERT: C 82 LEU cc_start: 0.9209 (mt) cc_final: 0.8772 (mp) REVERT: C 104 MET cc_start: 0.8286 (ttt) cc_final: 0.7943 (ttp) REVERT: C 105 LYS cc_start: 0.8747 (tttt) cc_final: 0.8492 (tttm) REVERT: C 174 ASN cc_start: 0.9014 (t0) cc_final: 0.8338 (t0) REVERT: C 210 GLU cc_start: 0.7710 (tt0) cc_final: 0.7431 (tt0) REVERT: C 247 TYR cc_start: 0.8709 (m-80) cc_final: 0.8474 (m-80) REVERT: E 82 LEU cc_start: 0.9193 (mt) cc_final: 0.8791 (mp) REVERT: E 105 LYS cc_start: 0.8755 (tttt) cc_final: 0.8462 (tttm) REVERT: E 174 ASN cc_start: 0.9022 (t0) cc_final: 0.8355 (t0) REVERT: E 210 GLU cc_start: 0.7696 (tt0) cc_final: 0.7428 (tt0) REVERT: E 237 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7550 (mmt90) REVERT: E 247 TYR cc_start: 0.8661 (m-80) cc_final: 0.8371 (m-80) REVERT: G 65 TYR cc_start: 0.8343 (m-80) cc_final: 0.7512 (m-80) REVERT: G 82 LEU cc_start: 0.9195 (mt) cc_final: 0.8808 (mp) REVERT: G 105 LYS cc_start: 0.8748 (tttt) cc_final: 0.8484 (tttm) REVERT: G 174 ASN cc_start: 0.9006 (t0) cc_final: 0.8333 (t0) REVERT: G 210 GLU cc_start: 0.7695 (tt0) cc_final: 0.7425 (tt0) REVERT: G 237 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7695 (mtt-85) REVERT: G 247 TYR cc_start: 0.8685 (m-80) cc_final: 0.8421 (m-80) outliers start: 33 outliers final: 24 residues processed: 405 average time/residue: 0.1352 time to fit residues: 80.9067 Evaluate side-chains 390 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 365 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 135 ARG Chi-restraints excluded: chain B residue 147 ASN 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 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 95 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 95 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 74 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.109690 restraints weight = 21654.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111845 restraints weight = 14923.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112331 restraints weight = 10831.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113525 restraints weight = 9527.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113607 restraints weight = 8437.092| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17168 Z= 0.178 Angle : 0.501 6.634 23186 Z= 0.265 Chirality : 0.048 0.150 2688 Planarity : 0.003 0.023 3000 Dihedral : 7.772 85.703 2540 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.40 % Allowed : 20.58 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.18), residues: 2140 helix: 0.78 (0.17), residues: 976 sheet: 0.37 (0.28), residues: 356 loop : -2.02 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 241 TYR 0.027 0.001 TYR E 33 PHE 0.009 0.001 PHE E 97 TRP 0.004 0.001 TRP A 46 HIS 0.003 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00435 (17168) covalent geometry : angle 0.50116 (23186) hydrogen bonds : bond 0.03467 ( 744) hydrogen bonds : angle 4.39781 ( 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 429 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 385 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8326 (m-80) cc_final: 0.7421 (m-80) REVERT: A 82 LEU cc_start: 0.9276 (mt) cc_final: 0.8851 (mp) REVERT: A 100 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8495 (t0) REVERT: A 105 LYS cc_start: 0.8760 (tttt) cc_final: 0.8487 (tttm) REVERT: A 174 ASN cc_start: 0.8976 (t0) cc_final: 0.8398 (t0) REVERT: A 200 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8516 (tttt) REVERT: A 237 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7613 (mmt90) REVERT: B 333 TYR cc_start: 0.8627 (t80) cc_final: 0.8282 (t80) REVERT: D 200 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8529 (tttt) REVERT: D 247 TYR cc_start: 0.8448 (m-80) cc_final: 0.8235 (m-80) REVERT: D 332 ASN cc_start: 0.7549 (m110) cc_final: 0.7308 (m110) REVERT: D 333 TYR cc_start: 0.8607 (t80) cc_final: 0.8219 (t80) REVERT: F 333 TYR cc_start: 0.8615 (t80) cc_final: 0.8254 (t80) REVERT: H 333 TYR cc_start: 0.8573 (t80) cc_final: 0.8301 (t80) REVERT: C 65 TYR cc_start: 0.8392 (m-80) cc_final: 0.7487 (m-80) REVERT: C 82 LEU cc_start: 0.9278 (mt) cc_final: 0.8851 (mp) REVERT: C 105 LYS cc_start: 0.8743 (tttt) cc_final: 0.8484 (tttm) REVERT: C 174 ASN cc_start: 0.8954 (t0) cc_final: 0.8369 (t0) REVERT: C 200 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8533 (tttt) REVERT: C 210 GLU cc_start: 0.7731 (tt0) cc_final: 0.7496 (tt0) REVERT: E 65 TYR cc_start: 0.8358 (m-80) cc_final: 0.7489 (m-80) REVERT: E 82 LEU cc_start: 0.9263 (mt) cc_final: 0.8834 (mp) REVERT: E 105 LYS cc_start: 0.8732 (tttt) cc_final: 0.8477 (tttm) REVERT: E 174 ASN cc_start: 0.8957 (t0) cc_final: 0.8336 (t0) REVERT: E 200 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8535 (tttt) REVERT: E 210 GLU cc_start: 0.7718 (tt0) cc_final: 0.7500 (tt0) REVERT: E 237 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7645 (mmt90) REVERT: G 65 TYR cc_start: 0.8370 (m-80) cc_final: 0.7471 (m-80) REVERT: G 82 LEU cc_start: 0.9288 (mt) cc_final: 0.8868 (mp) REVERT: G 105 LYS cc_start: 0.8758 (tttt) cc_final: 0.8480 (tttm) REVERT: G 174 ASN cc_start: 0.8962 (t0) cc_final: 0.8360 (t0) REVERT: G 210 GLU cc_start: 0.7703 (tt0) cc_final: 0.7485 (tt0) REVERT: G 237 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7791 (mtt90) REVERT: G 247 TYR cc_start: 0.8773 (m-80) cc_final: 0.8538 (m-80) outliers start: 44 outliers final: 33 residues processed: 408 average time/residue: 0.1298 time to fit residues: 79.9387 Evaluate side-chains 406 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 372 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 A residue 323 LYS 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 303 ILE Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain H residue 244 ASP 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 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 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 95 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 285 ILE 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: 0.9990 chunk 157 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.142790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113069 restraints weight = 21478.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115234 restraints weight = 17240.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116697 restraints weight = 12101.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116865 restraints weight = 10079.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.117268 restraints weight = 9379.583| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17168 Z= 0.108 Angle : 0.448 5.704 23186 Z= 0.237 Chirality : 0.046 0.145 2688 Planarity : 0.003 0.022 3000 Dihedral : 7.540 88.374 2540 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.57 % Allowed : 21.29 % Favored : 76.15 % 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 are not related in a simple way. whole: -0.16 (0.18), residues: 2140 helix: 1.12 (0.17), residues: 972 sheet: 0.44 (0.28), residues: 352 loop : -1.91 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 241 TYR 0.025 0.001 TYR A 33 PHE 0.009 0.001 PHE F 251 TRP 0.003 0.001 TRP A 52 HIS 0.001 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00258 (17168) covalent geometry : angle 0.44818 (23186) hydrogen bonds : bond 0.02739 ( 744) hydrogen bonds : angle 4.24123 ( 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 416 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 369 time to evaluate : 0.655 Fit side-chains REVERT: A 65 TYR cc_start: 0.8357 (m-80) cc_final: 0.7436 (m-80) REVERT: A 82 LEU cc_start: 0.9230 (mt) cc_final: 0.8813 (mp) REVERT: A 93 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7924 (mmm160) REVERT: A 100 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8529 (t0) REVERT: A 105 LYS cc_start: 0.8702 (tttt) cc_final: 0.8392 (tttm) REVERT: A 174 ASN cc_start: 0.9048 (t0) cc_final: 0.8406 (t0) REVERT: A 200 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8454 (tttt) REVERT: A 210 GLU cc_start: 0.7803 (tt0) cc_final: 0.7482 (tt0) REVERT: A 237 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7635 (mmt90) REVERT: B 200 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8389 (tttt) REVERT: B 333 TYR cc_start: 0.8527 (t80) cc_final: 0.8184 (t80) REVERT: D 200 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8506 (tttt) REVERT: D 247 TYR cc_start: 0.8440 (m-80) cc_final: 0.8233 (m-80) REVERT: D 333 TYR cc_start: 0.8535 (t80) cc_final: 0.8171 (t80) REVERT: F 333 TYR cc_start: 0.8585 (t80) cc_final: 0.8287 (t80) REVERT: H 333 TYR cc_start: 0.8541 (t80) cc_final: 0.8283 (t80) REVERT: C 65 TYR cc_start: 0.8430 (m-80) cc_final: 0.7563 (m-80) REVERT: C 82 LEU cc_start: 0.9244 (mt) cc_final: 0.8813 (mp) REVERT: C 105 LYS cc_start: 0.8679 (tttt) cc_final: 0.8387 (tttm) REVERT: C 174 ASN cc_start: 0.8984 (t0) cc_final: 0.8483 (t0) REVERT: C 200 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8422 (tttt) REVERT: C 210 GLU cc_start: 0.7775 (tt0) cc_final: 0.7501 (tt0) REVERT: C 247 TYR cc_start: 0.8799 (m-80) cc_final: 0.8587 (m-80) REVERT: E 65 TYR cc_start: 0.8416 (m-80) cc_final: 0.7544 (m-80) REVERT: E 82 LEU cc_start: 0.9263 (mt) cc_final: 0.8836 (mp) REVERT: E 105 LYS cc_start: 0.8683 (tttt) cc_final: 0.8379 (tttm) REVERT: E 174 ASN cc_start: 0.8989 (t0) cc_final: 0.8482 (t0) REVERT: E 200 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8418 (tttt) REVERT: E 210 GLU cc_start: 0.7769 (tt0) cc_final: 0.7497 (tt0) REVERT: E 237 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7653 (mmt90) REVERT: E 247 TYR cc_start: 0.8689 (m-80) cc_final: 0.8399 (m-80) REVERT: G 65 TYR cc_start: 0.8419 (m-80) cc_final: 0.7522 (m-80) REVERT: G 82 LEU cc_start: 0.9284 (mt) cc_final: 0.8866 (mp) REVERT: G 105 LYS cc_start: 0.8691 (tttt) cc_final: 0.8383 (tttm) REVERT: G 174 ASN cc_start: 0.8992 (t0) cc_final: 0.8471 (t0) REVERT: G 210 GLU cc_start: 0.7761 (tt0) cc_final: 0.7490 (tt0) REVERT: G 237 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7757 (mtt90) REVERT: G 247 TYR cc_start: 0.8745 (m-80) cc_final: 0.8466 (m-80) outliers start: 47 outliers final: 43 residues processed: 396 average time/residue: 0.1299 time to fit residues: 76.6630 Evaluate side-chains 404 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 360 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 LYS 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 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 95 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 119 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 119 VAL Chi-restraints excluded: chain E residue 265 VAL 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 95 LEU Chi-restraints excluded: chain G residue 106 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 159 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN F 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.149105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119340 restraints weight = 21102.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121945 restraints weight = 13786.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123870 restraints weight = 10274.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.125051 restraints weight = 8375.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125931 restraints weight = 7304.592| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17168 Z= 0.176 Angle : 0.494 5.212 23186 Z= 0.261 Chirality : 0.048 0.153 2688 Planarity : 0.003 0.039 3000 Dihedral : 7.666 88.346 2540 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.06 % Allowed : 21.18 % Favored : 75.76 % 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 are not related in a simple way. whole: -0.11 (0.18), residues: 2140 helix: 1.11 (0.17), residues: 980 sheet: 0.42 (0.28), residues: 356 loop : -1.81 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.025 0.001 TYR C 33 PHE 0.007 0.001 PHE D 140 TRP 0.004 0.001 TRP A 46 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00434 (17168) covalent geometry : angle 0.49400 (23186) hydrogen bonds : bond 0.03306 ( 744) hydrogen bonds : angle 4.34479 ( 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 427 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 371 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8346 (m-80) cc_final: 0.7460 (m-80) REVERT: A 93 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7927 (mmm160) REVERT: A 100 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8543 (t0) REVERT: A 105 LYS cc_start: 0.8727 (tttt) cc_final: 0.8506 (tttm) REVERT: A 111 ASP cc_start: 0.7178 (m-30) cc_final: 0.6911 (m-30) REVERT: A 174 ASN cc_start: 0.8928 (t0) cc_final: 0.8541 (t0) REVERT: A 237 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7596 (mmt90) REVERT: B 200 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8494 (tttt) REVERT: B 333 TYR cc_start: 0.8643 (t80) cc_final: 0.8306 (t80) REVERT: D 132 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7629 (ttm170) REVERT: D 247 TYR cc_start: 0.8658 (m-80) cc_final: 0.8436 (m-80) REVERT: D 333 TYR cc_start: 0.8636 (t80) cc_final: 0.8279 (t80) REVERT: F 332 ASN cc_start: 0.7419 (m110) cc_final: 0.7173 (m-40) REVERT: F 333 TYR cc_start: 0.8620 (t80) cc_final: 0.8365 (t80) REVERT: H 333 TYR cc_start: 0.8577 (t80) cc_final: 0.8342 (t80) REVERT: C 65 TYR cc_start: 0.8294 (m-80) cc_final: 0.7395 (m-80) REVERT: C 82 LEU cc_start: 0.9288 (mt) cc_final: 0.8840 (mp) REVERT: C 105 LYS cc_start: 0.8702 (tttt) cc_final: 0.8494 (tttm) REVERT: C 174 ASN cc_start: 0.8940 (t0) cc_final: 0.8563 (t0) REVERT: C 210 GLU cc_start: 0.7659 (tt0) cc_final: 0.7440 (tt0) REVERT: E 65 TYR cc_start: 0.8290 (m-80) cc_final: 0.7430 (m-80) REVERT: E 104 MET cc_start: 0.8333 (ttt) cc_final: 0.7972 (ttp) REVERT: E 105 LYS cc_start: 0.8763 (tttt) cc_final: 0.8495 (tttm) REVERT: E 174 ASN cc_start: 0.8941 (t0) cc_final: 0.8569 (t0) REVERT: E 200 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8475 (tttt) REVERT: E 210 GLU cc_start: 0.7652 (tt0) cc_final: 0.7432 (tt0) REVERT: E 237 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7597 (mmt90) REVERT: G 65 TYR cc_start: 0.8304 (m-80) cc_final: 0.7395 (m-80) REVERT: G 82 LEU cc_start: 0.9333 (mt) cc_final: 0.8889 (mp) REVERT: G 104 MET cc_start: 0.8322 (ttt) cc_final: 0.7954 (ttp) REVERT: G 174 ASN cc_start: 0.8947 (t0) cc_final: 0.8567 (t0) REVERT: G 210 GLU cc_start: 0.7650 (tt0) cc_final: 0.7433 (tt0) REVERT: G 237 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7686 (mtt90) outliers start: 56 outliers final: 43 residues processed: 409 average time/residue: 0.1323 time to fit residues: 80.4659 Evaluate side-chains 410 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 366 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 135 ARG 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 A residue 323 LYS 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 F residue 147 ASN Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain H residue 244 ASP 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 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 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 285 ILE 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: 2.9990 chunk 43 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.141543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111789 restraints weight = 21632.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112684 restraints weight = 19631.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114770 restraints weight = 14984.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114929 restraints weight = 11866.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.115238 restraints weight = 10490.287| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17168 Z= 0.139 Angle : 0.476 5.090 23186 Z= 0.252 Chirality : 0.047 0.148 2688 Planarity : 0.003 0.023 3000 Dihedral : 7.568 88.412 2540 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.78 % Allowed : 21.51 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2140 helix: 1.28 (0.17), residues: 972 sheet: 0.54 (0.28), residues: 352 loop : -1.83 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.025 0.001 TYR E 33 PHE 0.006 0.001 PHE D 140 TRP 0.003 0.001 TRP A 46 HIS 0.002 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00341 (17168) covalent geometry : angle 0.47620 (23186) hydrogen bonds : bond 0.02960 ( 744) hydrogen bonds : angle 4.29876 ( 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 427 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 376 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8463 (m-80) cc_final: 0.7519 (m-80) REVERT: A 93 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7972 (mmm160) REVERT: A 100 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8523 (t0) REVERT: A 105 LYS cc_start: 0.8767 (tttt) cc_final: 0.8425 (tttm) REVERT: A 111 ASP cc_start: 0.7484 (m-30) cc_final: 0.7194 (m-30) REVERT: A 174 ASN cc_start: 0.9022 (t0) cc_final: 0.8515 (t0) REVERT: A 237 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7634 (mmt90) REVERT: B 200 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8426 (tttt) REVERT: B 333 TYR cc_start: 0.8579 (t80) cc_final: 0.8210 (t80) REVERT: D 132 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7682 (ttm170) REVERT: D 247 TYR cc_start: 0.8623 (m-80) cc_final: 0.8395 (m-80) REVERT: D 309 ASP cc_start: 0.7481 (m-30) cc_final: 0.6881 (p0) REVERT: D 333 TYR cc_start: 0.8561 (t80) cc_final: 0.8183 (t80) REVERT: F 333 TYR cc_start: 0.8592 (t80) cc_final: 0.8286 (t80) REVERT: H 309 ASP cc_start: 0.7540 (m-30) cc_final: 0.6921 (p0) REVERT: H 333 TYR cc_start: 0.8530 (t80) cc_final: 0.8268 (t80) REVERT: C 65 TYR cc_start: 0.8436 (m-80) cc_final: 0.7504 (m-80) REVERT: C 82 LEU cc_start: 0.9265 (mt) cc_final: 0.8824 (mp) REVERT: C 104 MET cc_start: 0.8279 (ttt) cc_final: 0.7865 (ttp) REVERT: C 105 LYS cc_start: 0.8688 (tttt) cc_final: 0.8420 (tttm) REVERT: C 174 ASN cc_start: 0.9026 (t0) cc_final: 0.8540 (t0) REVERT: C 200 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8443 (tttt) REVERT: C 210 GLU cc_start: 0.7729 (tt0) cc_final: 0.7484 (tt0) REVERT: E 65 TYR cc_start: 0.8441 (m-80) cc_final: 0.7495 (m-80) REVERT: E 82 LEU cc_start: 0.9183 (mt) cc_final: 0.8812 (mp) REVERT: E 104 MET cc_start: 0.8283 (ttt) cc_final: 0.7870 (ttp) REVERT: E 105 LYS cc_start: 0.8754 (tttt) cc_final: 0.8418 (tttm) REVERT: E 174 ASN cc_start: 0.9039 (t0) cc_final: 0.8549 (t0) REVERT: E 200 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8434 (tttt) REVERT: E 210 GLU cc_start: 0.7724 (tt0) cc_final: 0.7488 (tt0) REVERT: E 237 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7658 (mmt90) REVERT: G 65 TYR cc_start: 0.8451 (m-80) cc_final: 0.7498 (m-80) REVERT: G 104 MET cc_start: 0.8269 (ttt) cc_final: 0.7848 (ttp) REVERT: G 111 ASP cc_start: 0.7450 (m-30) cc_final: 0.7123 (m-30) REVERT: G 172 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8499 (mmtp) REVERT: G 174 ASN cc_start: 0.9043 (t0) cc_final: 0.8532 (t0) REVERT: G 210 GLU cc_start: 0.7743 (tt0) cc_final: 0.7500 (tt0) REVERT: G 237 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7692 (mtt90) REVERT: G 247 TYR cc_start: 0.8817 (m-80) cc_final: 0.8549 (m-80) outliers start: 51 outliers final: 45 residues processed: 408 average time/residue: 0.1318 time to fit residues: 80.1757 Evaluate side-chains 417 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 115 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 LYS 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 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 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 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 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 119 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: 0.0970 chunk 152 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 211 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 161 optimal weight: 0.0570 chunk 192 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN F 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.143382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.113620 restraints weight = 21405.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115543 restraints weight = 15731.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116545 restraints weight = 11158.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.117111 restraints weight = 9895.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117609 restraints weight = 8937.200| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17168 Z= 0.089 Angle : 0.446 5.209 23186 Z= 0.236 Chirality : 0.046 0.178 2688 Planarity : 0.003 0.032 3000 Dihedral : 7.214 87.064 2540 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.13 % Allowed : 22.49 % 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 are not related in a simple way. whole: 0.24 (0.18), residues: 2140 helix: 1.49 (0.17), residues: 972 sheet: 0.62 (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 C 237 TYR 0.025 0.001 TYR A 33 PHE 0.009 0.001 PHE A 75 TRP 0.003 0.000 TRP A 52 HIS 0.001 0.000 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00207 (17168) covalent geometry : angle 0.44647 (23186) hydrogen bonds : bond 0.02479 ( 744) hydrogen bonds : angle 4.16884 ( 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 410 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 371 time to evaluate : 0.584 Fit side-chains REVERT: A 65 TYR cc_start: 0.8417 (m-80) cc_final: 0.7419 (m-80) REVERT: A 82 LEU cc_start: 0.9233 (mt) cc_final: 0.8810 (mp) REVERT: A 104 MET cc_start: 0.8224 (ttt) cc_final: 0.7836 (ttp) REVERT: A 105 LYS cc_start: 0.8736 (tttt) cc_final: 0.8445 (tttm) REVERT: A 111 ASP cc_start: 0.7413 (m-30) cc_final: 0.7103 (m-30) REVERT: A 172 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8488 (mmtp) REVERT: A 174 ASN cc_start: 0.8993 (t0) cc_final: 0.8730 (t0) REVERT: A 200 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8381 (tttt) REVERT: A 237 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7611 (mmt90) REVERT: B 200 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8405 (tttt) REVERT: B 309 ASP cc_start: 0.7450 (m-30) cc_final: 0.6782 (p0) REVERT: B 333 TYR cc_start: 0.8499 (t80) cc_final: 0.8154 (t80) REVERT: D 132 ARG cc_start: 0.7989 (ttp-170) cc_final: 0.7680 (ttm170) REVERT: D 309 ASP cc_start: 0.7438 (m-30) cc_final: 0.6768 (p0) REVERT: D 333 TYR cc_start: 0.8467 (t80) cc_final: 0.8135 (t80) REVERT: F 200 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8261 (tttt) REVERT: F 309 ASP cc_start: 0.7534 (m-30) cc_final: 0.6986 (p0) REVERT: F 333 TYR cc_start: 0.8528 (t80) cc_final: 0.8209 (t80) REVERT: H 132 ARG cc_start: 0.7869 (ttp-170) cc_final: 0.7507 (ttm170) REVERT: H 309 ASP cc_start: 0.7555 (m-30) cc_final: 0.6906 (p0) REVERT: H 333 TYR cc_start: 0.8493 (t80) cc_final: 0.8271 (t80) REVERT: C 65 TYR cc_start: 0.8490 (m-80) cc_final: 0.7517 (m-80) REVERT: C 82 LEU cc_start: 0.9243 (mt) cc_final: 0.8813 (mp) REVERT: C 104 MET cc_start: 0.8229 (ttt) cc_final: 0.7826 (ttp) REVERT: C 105 LYS cc_start: 0.8714 (tttt) cc_final: 0.8441 (tttm) REVERT: C 111 ASP cc_start: 0.7387 (m-30) cc_final: 0.7065 (m-30) REVERT: C 172 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8481 (mmtp) REVERT: C 174 ASN cc_start: 0.9006 (t0) cc_final: 0.8708 (t0) REVERT: C 200 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8364 (tttt) REVERT: C 210 GLU cc_start: 0.7725 (tt0) cc_final: 0.7440 (tt0) REVERT: C 247 TYR cc_start: 0.8752 (m-80) cc_final: 0.8541 (m-80) REVERT: E 65 TYR cc_start: 0.8436 (m-80) cc_final: 0.7494 (m-80) REVERT: E 82 LEU cc_start: 0.9160 (mt) cc_final: 0.8801 (mp) REVERT: E 104 MET cc_start: 0.8249 (ttt) cc_final: 0.7843 (ttp) REVERT: E 105 LYS cc_start: 0.8727 (tttt) cc_final: 0.8446 (tttm) REVERT: E 111 ASP cc_start: 0.7403 (m-30) cc_final: 0.7089 (m-30) REVERT: E 172 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8485 (mmtp) REVERT: E 174 ASN cc_start: 0.9010 (t0) cc_final: 0.8727 (t0) REVERT: E 200 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8418 (tttt) REVERT: E 210 GLU cc_start: 0.7719 (tt0) cc_final: 0.7437 (tt0) REVERT: E 237 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7577 (mmt90) REVERT: E 247 TYR cc_start: 0.8695 (m-80) cc_final: 0.8451 (m-80) REVERT: G 65 TYR cc_start: 0.8427 (m-80) cc_final: 0.7491 (m-80) REVERT: G 82 LEU cc_start: 0.9160 (mt) cc_final: 0.8799 (mp) REVERT: G 104 MET cc_start: 0.8216 (ttt) cc_final: 0.7805 (ttp) REVERT: G 111 ASP cc_start: 0.7382 (m-30) cc_final: 0.7076 (m-30) REVERT: G 172 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8497 (mmtp) REVERT: G 174 ASN cc_start: 0.9013 (t0) cc_final: 0.8725 (t0) REVERT: G 210 GLU cc_start: 0.7707 (tt0) cc_final: 0.7435 (tt0) REVERT: G 237 ARG cc_start: 0.7882 (mtt90) cc_final: 0.7609 (mmt90) REVERT: G 247 TYR cc_start: 0.8756 (m-80) cc_final: 0.8472 (m-80) outliers start: 39 outliers final: 30 residues processed: 395 average time/residue: 0.1351 time to fit residues: 79.2963 Evaluate side-chains 396 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 366 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 106 LEU 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 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 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 C residue 95 LEU Chi-restraints excluded: chain C residue 106 LEU 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 95 LEU Chi-restraints excluded: chain E residue 106 LEU 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 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: 3.9990 chunk 5 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.143716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.113997 restraints weight = 21241.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116519 restraints weight = 16645.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117870 restraints weight = 11261.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117908 restraints weight = 9899.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118132 restraints weight = 9095.443| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17168 Z= 0.107 Angle : 0.476 8.380 23186 Z= 0.247 Chirality : 0.047 0.226 2688 Planarity : 0.003 0.025 3000 Dihedral : 7.075 88.590 2540 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.80 % Allowed : 23.20 % Favored : 75.00 % 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 are not related in a simple way. whole: 0.29 (0.18), residues: 2140 helix: 1.51 (0.17), residues: 972 sheet: 0.66 (0.29), residues: 352 loop : -1.72 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.025 0.001 TYR G 33 PHE 0.013 0.001 PHE C 251 TRP 0.003 0.000 TRP A 46 HIS 0.001 0.000 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00258 (17168) covalent geometry : angle 0.47560 (23186) hydrogen bonds : bond 0.02659 ( 744) hydrogen bonds : angle 4.15652 ( 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 409 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 376 time to evaluate : 0.688 Fit side-chains REVERT: A 65 TYR cc_start: 0.8298 (m-80) cc_final: 0.7367 (m-80) REVERT: A 82 LEU cc_start: 0.9255 (mt) cc_final: 0.8829 (mp) REVERT: A 104 MET cc_start: 0.8250 (ttt) cc_final: 0.7898 (ttp) REVERT: A 105 LYS cc_start: 0.8730 (tttt) cc_final: 0.8509 (tttm) REVERT: A 111 ASP cc_start: 0.7332 (m-30) cc_final: 0.7084 (m-30) REVERT: A 174 ASN cc_start: 0.8961 (t0) cc_final: 0.8728 (t0) REVERT: A 200 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8457 (tttt) REVERT: A 237 ARG cc_start: 0.7864 (mtt90) cc_final: 0.7599 (mmt90) REVERT: B 200 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8455 (tttt) REVERT: B 309 ASP cc_start: 0.7411 (m-30) cc_final: 0.6868 (p0) REVERT: B 333 TYR cc_start: 0.8585 (t80) cc_final: 0.8262 (t80) REVERT: D 132 ARG cc_start: 0.7916 (ttp-170) cc_final: 0.7605 (ttm170) REVERT: D 264 MET cc_start: 0.8552 (ttt) cc_final: 0.8227 (mtp) REVERT: D 309 ASP cc_start: 0.7512 (m-30) cc_final: 0.6957 (p0) REVERT: D 333 TYR cc_start: 0.8545 (t80) cc_final: 0.8253 (t80) REVERT: F 200 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8344 (tttt) REVERT: F 309 ASP cc_start: 0.7442 (m-30) cc_final: 0.7038 (p0) REVERT: F 333 TYR cc_start: 0.8565 (t80) cc_final: 0.8225 (t80) REVERT: H 132 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7362 (ttm170) REVERT: H 309 ASP cc_start: 0.7491 (m-30) cc_final: 0.6971 (p0) REVERT: C 65 TYR cc_start: 0.8320 (m-80) cc_final: 0.7317 (m-80) REVERT: C 82 LEU cc_start: 0.9267 (mt) cc_final: 0.8833 (mp) REVERT: C 104 MET cc_start: 0.8300 (ttt) cc_final: 0.7944 (ttp) REVERT: C 105 LYS cc_start: 0.8710 (tttt) cc_final: 0.8504 (tttm) REVERT: C 111 ASP cc_start: 0.7220 (m-30) cc_final: 0.6941 (m-30) REVERT: C 174 ASN cc_start: 0.8968 (t0) cc_final: 0.8720 (t0) REVERT: C 200 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8425 (tttt) REVERT: C 210 GLU cc_start: 0.7637 (tt0) cc_final: 0.7373 (tt0) REVERT: C 247 TYR cc_start: 0.8786 (m-80) cc_final: 0.8549 (m-80) REVERT: E 65 TYR cc_start: 0.8303 (m-80) cc_final: 0.7391 (m-80) REVERT: E 82 LEU cc_start: 0.9192 (mt) cc_final: 0.8827 (mp) REVERT: E 104 MET cc_start: 0.8281 (ttt) cc_final: 0.7908 (ttp) REVERT: E 105 LYS cc_start: 0.8727 (tttt) cc_final: 0.8508 (tttm) REVERT: E 111 ASP cc_start: 0.7233 (m-30) cc_final: 0.6961 (m-30) REVERT: E 174 ASN cc_start: 0.8975 (t0) cc_final: 0.8739 (t0) REVERT: E 200 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8463 (tttt) REVERT: E 210 GLU cc_start: 0.7640 (tt0) cc_final: 0.7377 (tt0) REVERT: E 237 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7583 (mmt90) REVERT: E 247 TYR cc_start: 0.8756 (m-80) cc_final: 0.8478 (m-80) REVERT: G 65 TYR cc_start: 0.8306 (m-80) cc_final: 0.7375 (m-80) REVERT: G 82 LEU cc_start: 0.9191 (mt) cc_final: 0.8820 (mp) REVERT: G 104 MET cc_start: 0.8271 (ttt) cc_final: 0.7906 (ttp) REVERT: G 111 ASP cc_start: 0.7200 (m-30) cc_final: 0.6943 (m-30) REVERT: G 174 ASN cc_start: 0.8976 (t0) cc_final: 0.8736 (t0) REVERT: G 210 GLU cc_start: 0.7629 (tt0) cc_final: 0.7371 (tt0) REVERT: G 237 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7597 (mmt90) REVERT: G 247 TYR cc_start: 0.8804 (m-80) cc_final: 0.8586 (m-80) outliers start: 33 outliers final: 29 residues processed: 398 average time/residue: 0.1338 time to fit residues: 79.0386 Evaluate side-chains 402 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 373 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 106 LEU Chi-restraints excluded: chain A residue 115 SER 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 F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 LEU 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 95 LEU Chi-restraints excluded: chain E residue 106 LEU 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 189 SER 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: 7.9990 chunk 187 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.141797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.112184 restraints weight = 21445.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.114542 restraints weight = 17026.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116032 restraints weight = 11791.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.116069 restraints weight = 9899.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116361 restraints weight = 9253.531| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17168 Z= 0.130 Angle : 0.497 9.656 23186 Z= 0.255 Chirality : 0.048 0.271 2688 Planarity : 0.003 0.024 3000 Dihedral : 7.062 88.305 2540 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.97 % Allowed : 22.98 % 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 are not related in a simple way. whole: 0.28 (0.18), residues: 2140 helix: 1.49 (0.17), residues: 972 sheet: 0.68 (0.29), residues: 352 loop : -1.71 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.032 0.002 TYR A 33 PHE 0.011 0.001 PHE C 251 TRP 0.003 0.001 TRP A 46 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00318 (17168) covalent geometry : angle 0.49692 (23186) hydrogen bonds : bond 0.02916 ( 744) hydrogen bonds : angle 4.21090 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2867.49 seconds wall clock time: 49 minutes 59.63 seconds (2999.63 seconds total)