Starting phenix.real_space_refine on Sat Jul 4 00:15:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5bkj_9406/07_2026/5bkj_9406.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkj_9406/07_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_9406/07_2026/5bkj_9406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkj_9406/07_2026/5bkj_9406.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5bkj_9406/07_2026/5bkj_9406.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5bkj_9406/07_2026/5bkj_9406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5bkj_9406/07_2026/5bkj_9406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkj_9406/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 9 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: 9 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: 9 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: 9 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: 3.30, per 1000 atoms: 0.19 Number of scatterers: 16939 At special positions: 0 Unit cell: (150.7, 150.7, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 68 16.00 P 4 15.00 O 3276 8.00 N 2897 7.00 C 10692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 595.1 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: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.534A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 105 removed outlier: 3.758A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.830A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.597A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.634A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU D 171 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 230 through 240 removed outlier: 3.636A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.635A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.624A pdb=" N THR F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.770A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 147 through 156 removed outlier: 4.196A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 171 removed outlier: 3.564A pdb=" N GLU H 171 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.530A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.635A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.623A pdb=" N THR H 289 " --> pdb=" O ILE H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.771A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 105 removed outlier: 3.759A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.831A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.572A pdb=" N PHE C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.973A pdb=" N ALA E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 105 removed outlier: 3.759A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.831A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.662A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.618A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 325 through 334 removed outlier: 3.737A pdb=" N ARG E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.535A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 removed outlier: 3.972A pdb=" N ALA G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 105 removed outlier: 3.758A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.830A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.663A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.619A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.596A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 257 removed outlier: 3.573A pdb=" N PHE G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 325 through 334 removed outlier: 3.736A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR G 333 " --> pdb=" O ARG G 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 3.589A pdb=" N ASN A 158 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.873A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.511A pdb=" N GLY F 295 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.737A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.512A pdb=" N GLY H 295 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.590A pdb=" N ASN C 158 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.873A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.590A pdb=" N ASN E 158 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.872A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.589A pdb=" N ASN G 158 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.871A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.48 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: 9868 24.59 - 49.18: 520 49.18 - 73.77: 40 73.77 - 98.35: 20 98.35 - 122.94: 4 Dihedral angle restraints: 10452 sinusoidal: 4300 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 10449 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.520 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 14.990 122.943 6500 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/Z covalent geometry : bond 0.00584 / 0.26 (17168) covalent geometry : angle 0.81314 / 0.45 (23186) hydrogen bonds : bond 0.20029 / 13.40 ( 744) hydrogen bonds : angle 7.07524 / 4.97 ( 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 : 0.503 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: 0.1376 time to fit residues: 104.6265 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 : 0.489 ------------------------------------------------------------------------------- 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... 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 = 0.3628 r_free = 0.3628 target = 0.148584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118108 restraints weight = 21175.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121059 restraints weight = 13534.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.123112 restraints weight = 9914.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124433 restraints weight = 8015.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125340 restraints weight = 6945.837| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17168 Z= 0.128 Angle : 0.497 5.287 23186 Z= 0.266 Chirality : 0.046 0.147 2688 Planarity : 0.004 0.045 3000 Dihedral : 8.485 97.201 2504 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.86 % Allowed : 13.48 % Favored : 84.66 % 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: -2.27 (0.16), residues: 2140 helix: -1.03 (0.15), residues: 992 sheet: -0.16 (0.26), residues: 356 loop : -2.70 (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 0.012 0.001 PHE F 251 TRP 0.003 0.000 TRP D 123 HIS 0.009 0.001 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17168) covalent geometry : angle 0.49651 / 0.27 (23186) hydrogen bonds : bond 0.03620 / 2.41 ( 744) hydrogen bonds : angle 4.81650 / 3.35 ( 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 425 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 391 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8246 (m-80) cc_final: 0.7412 (m-80) REVERT: A 174 ASN cc_start: 0.8965 (t0) cc_final: 0.8404 (t0) REVERT: A 210 GLU cc_start: 0.7683 (tt0) cc_final: 0.7426 (tt0) REVERT: A 319 LEU cc_start: 0.9068 (tp) cc_final: 0.8853 (tp) REVERT: B 310 TYR cc_start: 0.8023 (t80) cc_final: 0.7792 (t80) REVERT: B 333 TYR cc_start: 0.8726 (t80) cc_final: 0.8222 (t80) REVERT: D 200 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8521 (tttt) REVERT: F 333 TYR cc_start: 0.8568 (t80) cc_final: 0.8224 (t80) REVERT: H 333 TYR cc_start: 0.8618 (t80) cc_final: 0.8210 (t80) REVERT: C 82 LEU cc_start: 0.9190 (mt) cc_final: 0.8784 (mp) REVERT: C 105 LYS cc_start: 0.8715 (tttt) cc_final: 0.8505 (tttm) REVERT: C 174 ASN cc_start: 0.8986 (t0) cc_final: 0.8446 (t0) REVERT: C 210 GLU cc_start: 0.7694 (tt0) cc_final: 0.7484 (tt0) REVERT: E 82 LEU cc_start: 0.9155 (mt) cc_final: 0.8782 (mp) REVERT: E 174 ASN cc_start: 0.8980 (t0) cc_final: 0.8434 (t0) REVERT: E 210 GLU cc_start: 0.7679 (tt0) cc_final: 0.7476 (tt0) REVERT: E 247 TYR cc_start: 0.8709 (m-80) cc_final: 0.8489 (m-80) REVERT: G 82 LEU cc_start: 0.9149 (mt) cc_final: 0.8793 (mp) REVERT: G 105 LYS cc_start: 0.8713 (tttt) cc_final: 0.8512 (tttm) REVERT: G 174 ASN cc_start: 0.8979 (t0) cc_final: 0.8429 (t0) REVERT: G 210 GLU cc_start: 0.7691 (tt0) cc_final: 0.7476 (tt0) outliers start: 34 outliers final: 22 residues processed: 413 average time/residue: 0.1412 time to fit residues: 84.8500 Evaluate side-chains 399 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 377 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 300 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 300 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 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 106 LEU 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: 0.8980 chunk 53 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3557 r_free = 0.3557 target = 0.142967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.111561 restraints weight = 21855.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114952 restraints weight = 15288.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115678 restraints weight = 10247.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.116186 restraints weight = 9017.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116511 restraints weight = 8421.233| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17168 Z= 0.142 Angle : 0.480 4.678 23186 Z= 0.255 Chirality : 0.047 0.148 2688 Planarity : 0.003 0.032 3000 Dihedral : 7.834 92.093 2504 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.24 % Allowed : 15.50 % Favored : 82.26 % 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: -1.49 (0.17), residues: 2140 helix: -0.25 (0.16), residues: 1008 sheet: 0.09 (0.27), residues: 356 loop : -2.45 (0.18), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 262 TYR 0.022 0.001 TYR C 33 PHE 0.007 0.001 PHE H 140 TRP 0.003 0.001 TRP A 123 HIS 0.008 0.001 HIS F 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (17168) covalent geometry : angle 0.47994 / 0.26 (23186) hydrogen bonds : bond 0.03410 / 2.28 ( 744) hydrogen bonds : angle 4.52754 / 3.14 ( 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 427 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 386 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8380 (m-80) cc_final: 0.7475 (m-80) REVERT: A 102 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 174 ASN cc_start: 0.9015 (t0) cc_final: 0.8317 (t0) REVERT: A 237 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7576 (mtt-85) REVERT: B 333 TYR cc_start: 0.8633 (t80) cc_final: 0.8170 (t80) REVERT: D 200 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8492 (tttt) REVERT: F 333 TYR cc_start: 0.8620 (t80) cc_final: 0.8288 (t80) REVERT: H 333 TYR cc_start: 0.8566 (t80) cc_final: 0.8185 (t80) REVERT: C 65 TYR cc_start: 0.8447 (m-80) cc_final: 0.7622 (m-80) REVERT: C 82 LEU cc_start: 0.9208 (mt) cc_final: 0.8790 (mp) REVERT: C 102 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8398 (mm-30) REVERT: C 105 LYS cc_start: 0.8784 (tttt) cc_final: 0.8438 (tttm) REVERT: C 174 ASN cc_start: 0.9040 (t0) cc_final: 0.8349 (t0) REVERT: C 210 GLU cc_start: 0.7815 (tt0) cc_final: 0.7571 (tt0) REVERT: C 319 LEU cc_start: 0.9070 (tp) cc_final: 0.8828 (tp) REVERT: E 82 LEU cc_start: 0.9189 (mt) cc_final: 0.8825 (mp) REVERT: E 104 MET cc_start: 0.8082 (mtt) cc_final: 0.7761 (ttp) REVERT: E 174 ASN cc_start: 0.9027 (t0) cc_final: 0.8339 (t0) REVERT: E 210 GLU cc_start: 0.7784 (tt0) cc_final: 0.7560 (tt0) REVERT: E 237 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7571 (mtt-85) REVERT: G 65 TYR cc_start: 0.8481 (m-80) cc_final: 0.7613 (m-80) REVERT: G 82 LEU cc_start: 0.9185 (mt) cc_final: 0.8827 (mp) REVERT: G 102 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8225 (mm-30) REVERT: G 105 LYS cc_start: 0.8661 (tttt) cc_final: 0.8389 (tttm) REVERT: G 174 ASN cc_start: 0.9019 (t0) cc_final: 0.8310 (t0) REVERT: G 210 GLU cc_start: 0.7793 (tt0) cc_final: 0.7555 (tt0) REVERT: G 247 TYR cc_start: 0.8786 (m-80) cc_final: 0.8517 (m-80) outliers start: 41 outliers final: 31 residues processed: 409 average time/residue: 0.1374 time to fit residues: 83.0767 Evaluate side-chains 407 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 376 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 265 VAL 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 303 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 ARG 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 95 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 53 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN D 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.109543 restraints weight = 21864.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.112959 restraints weight = 16718.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114245 restraints weight = 10425.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.114515 restraints weight = 8808.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114839 restraints weight = 8319.570| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17168 Z= 0.193 Angle : 0.510 4.660 23186 Z= 0.272 Chirality : 0.048 0.153 2688 Planarity : 0.003 0.025 3000 Dihedral : 8.038 89.975 2504 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.06 % Allowed : 17.90 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.17), residues: 2140 helix: 0.19 (0.16), residues: 1000 sheet: 0.19 (0.27), residues: 356 loop : -2.32 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 237 TYR 0.025 0.002 TYR C 33 PHE 0.010 0.001 PHE G 97 TRP 0.005 0.001 TRP G 123 HIS 0.003 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (17168) covalent geometry : angle 0.51033 / 0.27 (23186) hydrogen bonds : bond 0.03655 / 2.44 ( 744) hydrogen bonds : angle 4.56414 / 3.16 ( 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 437 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 381 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8341 (m-80) cc_final: 0.7421 (m-80) REVERT: A 100 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8489 (t0) REVERT: A 104 MET cc_start: 0.8105 (mtt) cc_final: 0.7778 (ttp) REVERT: A 174 ASN cc_start: 0.8962 (t0) cc_final: 0.8569 (t0) REVERT: A 237 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7588 (mtt-85) REVERT: B 200 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8482 (tttt) REVERT: B 333 TYR cc_start: 0.8704 (t80) cc_final: 0.8326 (t80) REVERT: D 200 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8420 (tttt) REVERT: D 333 TYR cc_start: 0.8702 (t80) cc_final: 0.8307 (t80) REVERT: F 333 TYR cc_start: 0.8663 (t80) cc_final: 0.8400 (t80) REVERT: H 333 TYR cc_start: 0.8609 (t80) cc_final: 0.8297 (t80) REVERT: C 65 TYR cc_start: 0.8340 (m-80) cc_final: 0.7447 (m-80) REVERT: C 82 LEU cc_start: 0.9282 (mt) cc_final: 0.8836 (mp) REVERT: C 105 LYS cc_start: 0.8786 (tttt) cc_final: 0.8511 (tttm) REVERT: C 174 ASN cc_start: 0.8983 (t0) cc_final: 0.8593 (t0) REVERT: C 319 LEU cc_start: 0.9161 (tp) cc_final: 0.8939 (tp) REVERT: E 65 TYR cc_start: 0.8379 (m-80) cc_final: 0.7488 (m-80) REVERT: E 100 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8546 (t0) REVERT: E 104 MET cc_start: 0.8155 (mtt) cc_final: 0.7765 (ttp) REVERT: E 174 ASN cc_start: 0.8981 (t0) cc_final: 0.8358 (t0) REVERT: E 237 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7647 (mtt-85) REVERT: G 65 TYR cc_start: 0.8378 (m-80) cc_final: 0.7493 (m-80) REVERT: G 82 LEU cc_start: 0.9310 (mt) cc_final: 0.8880 (mp) REVERT: G 104 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7952 (ttp) REVERT: G 105 LYS cc_start: 0.8793 (tttt) cc_final: 0.8474 (tttm) REVERT: G 174 ASN cc_start: 0.8979 (t0) cc_final: 0.8587 (t0) outliers start: 56 outliers final: 40 residues processed: 417 average time/residue: 0.1319 time to fit residues: 82.4392 Evaluate side-chains 412 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 369 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 308 ARG Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 SER 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 35 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER 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 57 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 285 ILE Chi-restraints excluded: chain G residue 296 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 74 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.142874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111739 restraints weight = 21485.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.114844 restraints weight = 14075.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116350 restraints weight = 8992.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116673 restraints weight = 7980.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116959 restraints weight = 7182.018| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2618 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= 0.122 Angle : 0.455 4.860 23186 Z= 0.242 Chirality : 0.046 0.147 2688 Planarity : 0.003 0.023 3000 Dihedral : 7.611 83.353 2504 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.11 % Allowed : 19.54 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.62 (0.18), residues: 2140 helix: 0.66 (0.17), residues: 988 sheet: 0.39 (0.28), residues: 352 loop : -2.19 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 237 TYR 0.024 0.001 TYR E 33 PHE 0.009 0.001 PHE F 251 TRP 0.003 0.001 TRP G 46 HIS 0.002 0.001 HIS F 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (17168) covalent geometry : angle 0.45503 / 0.24 (23186) hydrogen bonds : bond 0.02958 / 1.96 ( 744) hydrogen bonds : angle 4.38013 / 3.03 ( 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 423 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 366 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8353 (m-80) cc_final: 0.7434 (m-80) REVERT: A 82 LEU cc_start: 0.9240 (mt) cc_final: 0.8810 (mp) REVERT: A 100 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8504 (t0) REVERT: A 104 MET cc_start: 0.7989 (mtt) cc_final: 0.7622 (ttp) REVERT: A 174 ASN cc_start: 0.8956 (t0) cc_final: 0.8528 (t0) REVERT: A 200 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8534 (tttt) REVERT: A 210 GLU cc_start: 0.7603 (tt0) cc_final: 0.7266 (tt0) REVERT: B 200 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8427 (tttt) REVERT: B 333 TYR cc_start: 0.8601 (t80) cc_final: 0.8255 (t80) REVERT: D 200 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8416 (tttt) REVERT: D 333 TYR cc_start: 0.8563 (t80) cc_final: 0.8159 (t80) REVERT: F 333 TYR cc_start: 0.8596 (t80) cc_final: 0.8373 (t80) REVERT: H 247 TYR cc_start: 0.8307 (m-80) cc_final: 0.8019 (m-80) REVERT: H 333 TYR cc_start: 0.8521 (t80) cc_final: 0.8215 (t80) REVERT: C 65 TYR cc_start: 0.8384 (m-80) cc_final: 0.7499 (m-80) REVERT: C 82 LEU cc_start: 0.9256 (mt) cc_final: 0.8806 (mp) REVERT: C 105 LYS cc_start: 0.8730 (tttt) cc_final: 0.8431 (tttm) REVERT: C 174 ASN cc_start: 0.8986 (t0) cc_final: 0.8527 (t0) REVERT: E 65 TYR cc_start: 0.8358 (m-80) cc_final: 0.7474 (m-80) REVERT: E 100 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8539 (t0) REVERT: E 104 MET cc_start: 0.8004 (mtt) cc_final: 0.7634 (ttp) REVERT: E 174 ASN cc_start: 0.8992 (t0) cc_final: 0.8535 (t0) REVERT: G 65 TYR cc_start: 0.8351 (m-80) cc_final: 0.7492 (m-80) REVERT: G 100 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8524 (t0) REVERT: G 104 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7863 (ttp) REVERT: G 105 LYS cc_start: 0.8730 (tttt) cc_final: 0.8417 (tttm) REVERT: G 174 ASN cc_start: 0.8978 (t0) cc_final: 0.8526 (t0) REVERT: G 210 GLU cc_start: 0.7728 (tt0) cc_final: 0.7484 (tt0) REVERT: G 247 TYR cc_start: 0.8743 (m-80) cc_final: 0.8451 (m-80) outliers start: 57 outliers final: 46 residues processed: 398 average time/residue: 0.1304 time to fit residues: 78.2508 Evaluate side-chains 407 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 357 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 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 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 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 289 THR Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain H residue 303 ILE 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 265 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 100 ASN 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 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 110 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 130 optimal weight: 0.0010 chunk 75 optimal weight: 4.9990 overall best weight: 0.9906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.143410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112689 restraints weight = 21494.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114915 restraints weight = 16905.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116471 restraints weight = 11584.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116660 restraints weight = 9838.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117060 restraints weight = 9107.490| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17168 Z= 0.115 Angle : 0.449 4.478 23186 Z= 0.239 Chirality : 0.046 0.148 2688 Planarity : 0.003 0.040 3000 Dihedral : 7.070 68.393 2504 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.17 % Allowed : 20.03 % Favored : 76.80 % 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: 0.94 (0.17), residues: 996 sheet: 0.45 (0.28), residues: 352 loop : -1.99 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 237 TYR 0.026 0.001 TYR C 33 PHE 0.006 0.001 PHE G 75 TRP 0.003 0.001 TRP G 46 HIS 0.001 0.001 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (17168) covalent geometry : angle 0.44886 / 0.24 (23186) hydrogen bonds : bond 0.02809 / 1.87 ( 744) hydrogen bonds : angle 4.25147 / 2.94 ( 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 428 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 370 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8417 (m-80) cc_final: 0.7522 (m-80) REVERT: A 82 LEU cc_start: 0.9223 (mt) cc_final: 0.8795 (mp) REVERT: A 93 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7977 (mmm160) REVERT: A 100 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8479 (t0) REVERT: A 104 MET cc_start: 0.7919 (mtt) cc_final: 0.7527 (ttp) REVERT: A 111 ASP cc_start: 0.7543 (m-30) cc_final: 0.7232 (m-30) REVERT: A 174 ASN cc_start: 0.9013 (t0) cc_final: 0.8502 (t0) REVERT: A 200 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8472 (tttt) REVERT: A 247 TYR cc_start: 0.8656 (m-80) cc_final: 0.8373 (m-80) REVERT: B 200 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8421 (tttt) REVERT: B 333 TYR cc_start: 0.8546 (t80) cc_final: 0.8215 (t80) REVERT: D 132 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7518 (ttm170) REVERT: D 200 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8402 (tttt) REVERT: D 333 TYR cc_start: 0.8535 (t80) cc_final: 0.8176 (t80) REVERT: H 333 TYR cc_start: 0.8490 (t80) cc_final: 0.8217 (t80) REVERT: C 65 TYR cc_start: 0.8415 (m-80) cc_final: 0.7541 (m-80) REVERT: C 82 LEU cc_start: 0.9240 (mt) cc_final: 0.8799 (mp) REVERT: C 105 LYS cc_start: 0.8663 (tttt) cc_final: 0.8362 (tttm) REVERT: C 174 ASN cc_start: 0.8997 (t0) cc_final: 0.8465 (t0) REVERT: C 247 TYR cc_start: 0.8755 (m-80) cc_final: 0.8548 (m-80) REVERT: E 65 TYR cc_start: 0.8405 (m-80) cc_final: 0.7537 (m-80) REVERT: E 82 LEU cc_start: 0.9221 (mt) cc_final: 0.8803 (mp) REVERT: E 100 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8520 (t0) REVERT: E 104 MET cc_start: 0.7919 (mtt) cc_final: 0.7510 (ttp) REVERT: E 174 ASN cc_start: 0.8997 (t0) cc_final: 0.8468 (t0) REVERT: E 247 TYR cc_start: 0.8725 (m-80) cc_final: 0.8413 (m-80) REVERT: G 65 TYR cc_start: 0.8390 (m-80) cc_final: 0.7531 (m-80) REVERT: G 82 LEU cc_start: 0.9158 (mt) cc_final: 0.8799 (mp) REVERT: G 100 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8510 (t0) REVERT: G 104 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7741 (ttp) REVERT: G 105 LYS cc_start: 0.8671 (tttt) cc_final: 0.8349 (tttm) REVERT: G 111 ASP cc_start: 0.7485 (m-30) cc_final: 0.7183 (m-30) REVERT: G 174 ASN cc_start: 0.9023 (t0) cc_final: 0.8510 (t0) REVERT: G 210 GLU cc_start: 0.7773 (tt0) cc_final: 0.7490 (tt0) REVERT: G 247 TYR cc_start: 0.8746 (m-80) cc_final: 0.8461 (m-80) outliers start: 58 outliers final: 48 residues processed: 403 average time/residue: 0.1340 time to fit residues: 80.8396 Evaluate side-chains 412 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 135 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 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 F residue 147 ASN Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 289 THR 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 115 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 323 LYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 159 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3580 r_free = 0.3580 target = 0.144978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114642 restraints weight = 21367.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117800 restraints weight = 16126.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119020 restraints weight = 10597.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119465 restraints weight = 8600.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119726 restraints weight = 8132.832| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17168 Z= 0.101 Angle : 0.441 4.485 23186 Z= 0.234 Chirality : 0.046 0.143 2688 Planarity : 0.002 0.026 3000 Dihedral : 6.587 58.675 2504 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.06 % Allowed : 19.87 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.18), residues: 2140 helix: 1.34 (0.17), residues: 972 sheet: 0.51 (0.29), residues: 352 loop : -1.83 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 237 TYR 0.023 0.001 TYR E 33 PHE 0.008 0.001 PHE F 251 TRP 0.003 0.000 TRP G 46 HIS 0.001 0.000 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (17168) covalent geometry : angle 0.44137 / 0.23 (23186) hydrogen bonds : bond 0.02645 / 1.76 ( 744) hydrogen bonds : angle 4.17278 / 2.89 ( 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 430 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 374 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8376 (m-80) cc_final: 0.7458 (m-80) REVERT: A 82 LEU cc_start: 0.9227 (mt) cc_final: 0.8811 (mp) REVERT: A 93 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7945 (mmm160) REVERT: A 100 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8512 (t0) REVERT: A 104 MET cc_start: 0.7918 (mtt) cc_final: 0.7540 (ttp) REVERT: A 111 ASP cc_start: 0.7468 (m-30) cc_final: 0.7170 (m-30) REVERT: A 174 ASN cc_start: 0.9007 (t0) cc_final: 0.8497 (t0) REVERT: A 200 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8422 (tttt) REVERT: A 210 GLU cc_start: 0.7588 (tt0) cc_final: 0.7200 (tt0) REVERT: A 237 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7657 (mmt90) REVERT: A 247 TYR cc_start: 0.8666 (m-80) cc_final: 0.8413 (m-80) REVERT: B 200 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8425 (tttt) REVERT: B 309 ASP cc_start: 0.7441 (m-30) cc_final: 0.6758 (p0) REVERT: B 333 TYR cc_start: 0.8546 (t80) cc_final: 0.8239 (t80) REVERT: D 132 ARG cc_start: 0.7907 (ttp-170) cc_final: 0.7468 (ttm170) REVERT: D 200 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8449 (tttt) REVERT: D 247 TYR cc_start: 0.8614 (m-80) cc_final: 0.8337 (m-80) REVERT: D 333 TYR cc_start: 0.8537 (t80) cc_final: 0.8196 (t80) REVERT: H 132 ARG cc_start: 0.7884 (ttp-170) cc_final: 0.7447 (ttm170) REVERT: H 333 TYR cc_start: 0.8520 (t80) cc_final: 0.8290 (t80) REVERT: C 65 TYR cc_start: 0.8448 (m-80) cc_final: 0.7561 (m-80) REVERT: C 82 LEU cc_start: 0.9249 (mt) cc_final: 0.8810 (mp) REVERT: C 104 MET cc_start: 0.8233 (ttt) cc_final: 0.7832 (ttp) REVERT: C 105 LYS cc_start: 0.8716 (tttt) cc_final: 0.8423 (tttm) REVERT: C 111 ASP cc_start: 0.7402 (m-30) cc_final: 0.7113 (m-30) REVERT: C 174 ASN cc_start: 0.9018 (t0) cc_final: 0.8499 (t0) REVERT: C 247 TYR cc_start: 0.8764 (m-80) cc_final: 0.8540 (m-80) REVERT: E 65 TYR cc_start: 0.8353 (m-80) cc_final: 0.7489 (m-80) REVERT: E 82 LEU cc_start: 0.9236 (mt) cc_final: 0.8824 (mp) REVERT: E 104 MET cc_start: 0.7888 (mtt) cc_final: 0.7524 (ttp) REVERT: E 111 ASP cc_start: 0.7451 (m-30) cc_final: 0.7157 (m-30) REVERT: E 174 ASN cc_start: 0.9021 (t0) cc_final: 0.8503 (t0) REVERT: E 237 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7598 (mmt90) REVERT: E 247 TYR cc_start: 0.8730 (m-80) cc_final: 0.8467 (m-80) REVERT: E 264 MET cc_start: 0.8521 (ttm) cc_final: 0.8244 (ttt) REVERT: G 65 TYR cc_start: 0.8366 (m-80) cc_final: 0.7498 (m-80) REVERT: G 82 LEU cc_start: 0.9163 (mt) cc_final: 0.8805 (mp) REVERT: G 100 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8526 (t0) REVERT: G 104 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7801 (ttp) REVERT: G 105 LYS cc_start: 0.8734 (tttt) cc_final: 0.8429 (tttm) REVERT: G 111 ASP cc_start: 0.7408 (m-30) cc_final: 0.7105 (m-30) REVERT: G 172 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8482 (mmtp) REVERT: G 174 ASN cc_start: 0.9012 (t0) cc_final: 0.8494 (t0) REVERT: G 210 GLU cc_start: 0.7740 (tt0) cc_final: 0.7448 (tt0) REVERT: G 247 TYR cc_start: 0.8752 (m-80) cc_final: 0.8432 (m-80) outliers start: 56 outliers final: 46 residues processed: 406 average time/residue: 0.1253 time to fit residues: 76.3120 Evaluate side-chains 408 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 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 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 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 265 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain 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 G residue 95 LEU Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 177 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.144522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114218 restraints weight = 21528.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115920 restraints weight = 17208.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117905 restraints weight = 12324.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.118178 restraints weight = 9975.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118685 restraints weight = 9387.358| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17168 Z= 0.101 Angle : 0.460 6.331 23186 Z= 0.241 Chirality : 0.047 0.195 2688 Planarity : 0.003 0.032 3000 Dihedral : 6.166 56.132 2504 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.00 % Allowed : 20.85 % 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: 0.18 (0.18), residues: 2140 helix: 1.45 (0.17), residues: 972 sheet: 0.57 (0.29), residues: 352 loop : -1.78 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 237 TYR 0.024 0.001 TYR A 33 PHE 0.013 0.001 PHE A 251 TRP 0.003 0.000 TRP C 52 HIS 0.001 0.000 HIS F 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (17168) covalent geometry : angle 0.45973 / 0.24 (23186) hydrogen bonds : bond 0.02619 / 1.74 ( 744) hydrogen bonds : angle 4.12431 / 2.86 ( 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: 55 poor density : 372 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 65 TYR cc_start: 0.8445 (m-80) cc_final: 0.7506 (m-80) REVERT: A 82 LEU cc_start: 0.9219 (mt) cc_final: 0.8800 (mp) REVERT: A 93 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7949 (mmm160) REVERT: A 104 MET cc_start: 0.7889 (mtt) cc_final: 0.7525 (ttp) REVERT: A 111 ASP cc_start: 0.7509 (m-30) cc_final: 0.7175 (m-30) REVERT: A 172 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8459 (mmtp) REVERT: A 174 ASN cc_start: 0.8997 (t0) cc_final: 0.8687 (t0) REVERT: A 200 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8355 (tttt) REVERT: A 237 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7650 (mmt90) REVERT: A 247 TYR cc_start: 0.8672 (m-80) cc_final: 0.8336 (m-80) REVERT: B 200 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8403 (tttt) REVERT: B 309 ASP cc_start: 0.7503 (m-30) cc_final: 0.6784 (p0) REVERT: B 333 TYR cc_start: 0.8513 (t80) cc_final: 0.8215 (t80) REVERT: D 132 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7470 (ttm170) REVERT: D 200 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8487 (tttt) REVERT: D 247 TYR cc_start: 0.8591 (m-80) cc_final: 0.8329 (m-80) REVERT: D 309 ASP cc_start: 0.7466 (m-30) cc_final: 0.6760 (p0) REVERT: D 333 TYR cc_start: 0.8479 (t80) cc_final: 0.8147 (t80) REVERT: H 132 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.7462 (ttm170) REVERT: H 309 ASP cc_start: 0.7516 (m-30) cc_final: 0.6763 (p0) REVERT: H 333 TYR cc_start: 0.8485 (t80) cc_final: 0.8262 (t80) REVERT: C 65 TYR cc_start: 0.8486 (m-80) cc_final: 0.7560 (m-80) REVERT: C 82 LEU cc_start: 0.9238 (mt) cc_final: 0.8804 (mp) REVERT: C 96 GLU cc_start: 0.7684 (tt0) cc_final: 0.7396 (tt0) REVERT: C 104 MET cc_start: 0.8207 (ttt) cc_final: 0.7798 (ttp) REVERT: C 105 LYS cc_start: 0.8691 (tttt) cc_final: 0.8382 (tttm) REVERT: C 111 ASP cc_start: 0.7467 (m-30) cc_final: 0.7148 (m-30) REVERT: C 172 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8460 (mmtp) REVERT: C 174 ASN cc_start: 0.9006 (t0) cc_final: 0.8697 (t0) REVERT: C 247 TYR cc_start: 0.8762 (m-80) cc_final: 0.8496 (m-80) REVERT: E 65 TYR cc_start: 0.8389 (m-80) cc_final: 0.7514 (m-80) REVERT: E 82 LEU cc_start: 0.9229 (mt) cc_final: 0.8819 (mp) REVERT: E 104 MET cc_start: 0.7846 (mtt) cc_final: 0.7487 (ttp) REVERT: E 111 ASP cc_start: 0.7488 (m-30) cc_final: 0.7159 (m-30) REVERT: E 172 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8447 (mmtp) REVERT: E 174 ASN cc_start: 0.9009 (t0) cc_final: 0.8699 (t0) REVERT: E 237 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7621 (mmt90) REVERT: E 247 TYR cc_start: 0.8713 (m-80) cc_final: 0.8371 (m-80) REVERT: G 65 TYR cc_start: 0.8413 (m-80) cc_final: 0.7502 (m-80) REVERT: G 82 LEU cc_start: 0.9150 (mt) cc_final: 0.8797 (mp) REVERT: G 100 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8519 (t0) REVERT: G 104 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7745 (ttp) REVERT: G 105 LYS cc_start: 0.8701 (tttt) cc_final: 0.8386 (tttm) REVERT: G 111 ASP cc_start: 0.7460 (m-30) cc_final: 0.7147 (m-30) REVERT: G 172 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8476 (mmtp) REVERT: G 174 ASN cc_start: 0.9004 (t0) cc_final: 0.8692 (t0) REVERT: G 210 GLU cc_start: 0.7746 (tt0) cc_final: 0.7454 (tt0) REVERT: G 247 TYR cc_start: 0.8738 (m-80) cc_final: 0.8409 (m-80) outliers start: 55 outliers final: 42 residues processed: 406 average time/residue: 0.1288 time to fit residues: 77.9152 Evaluate side-chains 407 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 363 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 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 F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 300 ASP Chi-restraints excluded: chain 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 265 VAL 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 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 321 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 50 optimal weight: 0.0980 chunk 152 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 118 optimal weight: 0.0970 chunk 3 optimal weight: 4.9990 chunk 82 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.145375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115699 restraints weight = 21357.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117875 restraints weight = 16722.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119384 restraints weight = 11628.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119818 restraints weight = 9654.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120201 restraints weight = 8859.253| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17168 Z= 0.084 Angle : 0.463 8.408 23186 Z= 0.238 Chirality : 0.046 0.247 2688 Planarity : 0.002 0.024 3000 Dihedral : 5.813 57.593 2504 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.51 % Allowed : 21.72 % 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: 0.30 (0.18), residues: 2140 helix: 1.57 (0.17), residues: 968 sheet: 0.65 (0.29), residues: 352 loop : -1.76 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 237 TYR 0.025 0.001 TYR G 33 PHE 0.015 0.001 PHE F 251 TRP 0.003 0.000 TRP G 52 HIS 0.001 0.000 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.08 (17168) covalent geometry : angle 0.46279 / 0.24 (23186) hydrogen bonds : bond 0.02418 / 1.60 ( 744) hydrogen bonds : angle 4.08791 / 2.84 ( 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 423 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 377 time to evaluate : 0.500 Fit side-chains REVERT: A 65 TYR cc_start: 0.8404 (m-80) cc_final: 0.7468 (m-80) REVERT: A 82 LEU cc_start: 0.9231 (mt) cc_final: 0.8816 (mp) REVERT: A 93 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7927 (mmm160) REVERT: A 104 MET cc_start: 0.7890 (mtt) cc_final: 0.7552 (ttp) REVERT: A 111 ASP cc_start: 0.7412 (m-30) cc_final: 0.7101 (m-30) REVERT: A 172 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8456 (mmtp) REVERT: A 174 ASN cc_start: 0.8988 (t0) cc_final: 0.8700 (t0) REVERT: A 200 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8352 (tttt) REVERT: A 237 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7599 (mmt90) REVERT: A 247 TYR cc_start: 0.8648 (m-80) cc_final: 0.8355 (m-80) REVERT: B 200 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8421 (tttt) REVERT: B 309 ASP cc_start: 0.7486 (m-30) cc_final: 0.6788 (p0) REVERT: B 333 TYR cc_start: 0.8481 (t80) cc_final: 0.8224 (t80) REVERT: D 132 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7400 (ttm170) REVERT: D 200 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8512 (tttt) REVERT: D 247 TYR cc_start: 0.8550 (m-80) cc_final: 0.8335 (m-80) REVERT: D 309 ASP cc_start: 0.7486 (m-30) cc_final: 0.6774 (p0) REVERT: D 333 TYR cc_start: 0.8444 (t80) cc_final: 0.8167 (t80) REVERT: F 200 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8074 (tttm) REVERT: F 309 ASP cc_start: 0.7538 (m-30) cc_final: 0.6987 (p0) REVERT: H 132 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7442 (ttm170) REVERT: H 309 ASP cc_start: 0.7575 (m-30) cc_final: 0.6852 (p0) REVERT: C 65 TYR cc_start: 0.8436 (m-80) cc_final: 0.7490 (m-80) REVERT: C 82 LEU cc_start: 0.9238 (mt) cc_final: 0.8806 (mp) REVERT: C 104 MET cc_start: 0.8243 (ttt) cc_final: 0.7848 (ttp) REVERT: C 105 LYS cc_start: 0.8668 (tttt) cc_final: 0.8397 (tttm) REVERT: C 111 ASP cc_start: 0.7369 (m-30) cc_final: 0.7076 (m-30) REVERT: C 172 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8436 (mmtp) REVERT: C 174 ASN cc_start: 0.8998 (t0) cc_final: 0.8701 (t0) REVERT: C 247 TYR cc_start: 0.8722 (m-80) cc_final: 0.8473 (m-80) REVERT: E 65 TYR cc_start: 0.8383 (m-80) cc_final: 0.7431 (m-80) REVERT: E 82 LEU cc_start: 0.9232 (mt) cc_final: 0.8830 (mp) REVERT: E 104 MET cc_start: 0.7881 (mtt) cc_final: 0.7571 (ttp) REVERT: E 111 ASP cc_start: 0.7397 (m-30) cc_final: 0.7095 (m-30) REVERT: E 172 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8456 (mmtp) REVERT: E 174 ASN cc_start: 0.9001 (t0) cc_final: 0.8699 (t0) REVERT: E 237 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7579 (mmt90) REVERT: E 247 TYR cc_start: 0.8682 (m-80) cc_final: 0.8385 (m-80) REVERT: G 65 TYR cc_start: 0.8363 (m-80) cc_final: 0.7419 (m-80) REVERT: G 82 LEU cc_start: 0.9155 (mt) cc_final: 0.8796 (mp) REVERT: G 100 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8584 (t0) REVERT: G 104 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7735 (ttp) REVERT: G 105 LYS cc_start: 0.8689 (tttt) cc_final: 0.8409 (tttm) REVERT: G 111 ASP cc_start: 0.7369 (m-30) cc_final: 0.7080 (m-30) REVERT: G 172 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8456 (mmtp) REVERT: G 174 ASN cc_start: 0.8996 (t0) cc_final: 0.8702 (t0) REVERT: G 210 GLU cc_start: 0.7715 (tt0) cc_final: 0.7419 (tt0) REVERT: G 247 TYR cc_start: 0.8712 (m-80) cc_final: 0.8463 (m-80) outliers start: 46 outliers final: 33 residues processed: 404 average time/residue: 0.1310 time to fit residues: 78.3799 Evaluate side-chains 404 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 369 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 189 SER 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 F residue 147 ASN Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain 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 265 VAL 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 119 VAL Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.154185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124651 restraints weight = 20767.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127538 restraints weight = 13339.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129547 restraints weight = 9806.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130763 restraints weight = 7929.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.131545 restraints weight = 6880.915| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17168 Z= 0.100 Angle : 0.473 8.528 23186 Z= 0.243 Chirality : 0.047 0.228 2688 Planarity : 0.002 0.029 3000 Dihedral : 5.689 59.491 2504 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.02 % Allowed : 22.60 % 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: 0.38 (0.18), residues: 2140 helix: 1.63 (0.17), residues: 968 sheet: 0.74 (0.29), residues: 352 loop : -1.72 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.030 0.001 TYR A 33 PHE 0.009 0.001 PHE F 251 TRP 0.003 0.000 TRP C 52 HIS 0.001 0.000 HIS B 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (17168) covalent geometry : angle 0.47290 / 0.24 (23186) hydrogen bonds : bond 0.02588 / 1.72 ( 744) hydrogen bonds : angle 4.07098 / 2.82 ( 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 416 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 0.474 Fit side-chains REVERT: A 65 TYR cc_start: 0.8426 (m-80) cc_final: 0.7503 (m-80) REVERT: A 82 LEU cc_start: 0.9208 (mt) cc_final: 0.8802 (mp) REVERT: A 104 MET cc_start: 0.7916 (mtt) cc_final: 0.7590 (ttp) REVERT: A 111 ASP cc_start: 0.7432 (m-30) cc_final: 0.7164 (m-30) REVERT: A 172 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8471 (mmtp) REVERT: A 174 ASN cc_start: 0.8993 (t0) cc_final: 0.8712 (t0) REVERT: A 200 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8364 (tttt) REVERT: A 237 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7597 (mmt90) REVERT: A 247 TYR cc_start: 0.8694 (m-80) cc_final: 0.8389 (m-80) REVERT: B 200 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8430 (tttt) REVERT: B 309 ASP cc_start: 0.7495 (m-30) cc_final: 0.6859 (p0) REVERT: B 333 TYR cc_start: 0.8449 (t80) cc_final: 0.8203 (t80) REVERT: D 132 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7457 (ttm170) REVERT: D 200 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8487 (tttt) REVERT: D 309 ASP cc_start: 0.7514 (m-30) cc_final: 0.6952 (p0) REVERT: D 333 TYR cc_start: 0.8445 (t80) cc_final: 0.8163 (t80) REVERT: F 309 ASP cc_start: 0.7448 (m-30) cc_final: 0.7028 (p0) REVERT: H 132 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7428 (ttm170) REVERT: H 309 ASP cc_start: 0.7526 (m-30) cc_final: 0.6947 (p0) REVERT: C 65 TYR cc_start: 0.8453 (m-80) cc_final: 0.7513 (m-80) REVERT: C 82 LEU cc_start: 0.9219 (mt) cc_final: 0.8796 (mp) REVERT: C 104 MET cc_start: 0.8255 (ttt) cc_final: 0.7853 (ttp) REVERT: C 105 LYS cc_start: 0.8652 (tttt) cc_final: 0.8383 (tttm) REVERT: C 111 ASP cc_start: 0.7393 (m-30) cc_final: 0.7143 (m-30) REVERT: C 174 ASN cc_start: 0.8999 (t0) cc_final: 0.8711 (t0) REVERT: C 247 TYR cc_start: 0.8738 (m-80) cc_final: 0.8493 (m-80) REVERT: E 65 TYR cc_start: 0.8430 (m-80) cc_final: 0.7497 (m-80) REVERT: E 82 LEU cc_start: 0.9212 (mt) cc_final: 0.8821 (mp) REVERT: E 104 MET cc_start: 0.7878 (mtt) cc_final: 0.7591 (ttp) REVERT: E 111 ASP cc_start: 0.7319 (m-30) cc_final: 0.7033 (m-30) REVERT: E 172 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8470 (mmtp) REVERT: E 174 ASN cc_start: 0.8995 (t0) cc_final: 0.8692 (t0) REVERT: E 237 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7591 (mmt90) REVERT: E 247 TYR cc_start: 0.8724 (m-80) cc_final: 0.8456 (m-80) REVERT: G 65 TYR cc_start: 0.8390 (m-80) cc_final: 0.7455 (m-80) REVERT: G 82 LEU cc_start: 0.9137 (mt) cc_final: 0.8785 (mp) REVERT: G 100 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8646 (t0) REVERT: G 104 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7745 (ttp) REVERT: G 105 LYS cc_start: 0.8671 (tttt) cc_final: 0.8395 (tttm) REVERT: G 111 ASP cc_start: 0.7393 (m-30) cc_final: 0.7146 (m-30) REVERT: G 174 ASN cc_start: 0.8990 (t0) cc_final: 0.8692 (t0) REVERT: G 210 GLU cc_start: 0.7736 (tt0) cc_final: 0.7444 (tt0) REVERT: G 247 TYR cc_start: 0.8736 (m-80) cc_final: 0.8485 (m-80) outliers start: 37 outliers final: 30 residues processed: 399 average time/residue: 0.1231 time to fit residues: 73.1777 Evaluate side-chains 399 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 367 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 189 SER 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 F residue 244 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 119 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain E residue 95 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 100 ASN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 321 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 147 optimal weight: 0.3980 chunk 187 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 99 optimal weight: 0.0270 chunk 83 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124938 restraints weight = 20792.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127845 restraints weight = 13284.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129726 restraints weight = 9781.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131104 restraints weight = 7929.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131862 restraints weight = 6874.381| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17168 Z= 0.096 Angle : 0.471 8.229 23186 Z= 0.242 Chirality : 0.047 0.214 2688 Planarity : 0.002 0.025 3000 Dihedral : 5.563 57.423 2504 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.07 % Allowed : 22.98 % Favored : 74.95 % 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: 0.45 (0.18), residues: 2140 helix: 1.68 (0.17), residues: 972 sheet: 0.76 (0.29), residues: 344 loop : -1.67 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.030 0.002 TYR C 33 PHE 0.012 0.001 PHE A 251 TRP 0.003 0.000 TRP G 52 HIS 0.001 0.000 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (17168) covalent geometry : angle 0.47106 / 0.24 (23186) hydrogen bonds : bond 0.02549 / 1.69 ( 744) hydrogen bonds : angle 4.05532 / 2.81 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2844.80 seconds wall clock time: 49 minutes 45.49 seconds (2985.49 seconds total)