Starting phenix.real_space_refine on Thu Feb 5 01:51:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3m_62787/02_2026/9l3m_62787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3m_62787/02_2026/9l3m_62787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l3m_62787/02_2026/9l3m_62787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3m_62787/02_2026/9l3m_62787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l3m_62787/02_2026/9l3m_62787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3m_62787/02_2026/9l3m_62787.map" } resolution = 2.86 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= 0.012 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 P 18 5.49 5 Mg 6 5.21 5 S 71 5.16 5 C 8999 2.51 5 N 2418 2.21 5 O 2741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14253 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2206 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 13, 'TRANS': 266} Chain breaks: 1 Chain: "B" Number of atoms: 2345 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 296, 2334 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 296, 2334 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 13, 'TRANS': 282} Chain breaks: 1 bond proxies already assigned to first conformer: 2360 Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2360 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 14, 'TRANS': 285} Chain breaks: 1 Chain: "D" Number of atoms: 2378 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 300, 2367 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 300, 2367 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 13, 'TRANS': 286} Chain breaks: 1 bond proxies already assigned to first conformer: 2393 Chain: "E" Number of atoms: 2361 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 298, 2350 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 298, 2350 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 bond proxies already assigned to first conformer: 2376 Chain: "F" Number of atoms: 2341 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2330 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 295, 2330 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 bond proxies already assigned to first conformer: 2355 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG B 74 " occ=0.46 ... (20 atoms not shown) pdb=" NH2BARG B 74 " occ=0.54 residue: pdb=" N AARG D 74 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG D 74 " occ=0.49 residue: pdb=" N AARG E 74 " occ=0.59 ... (20 atoms not shown) pdb=" NH2BARG E 74 " occ=0.41 residue: pdb=" N AARG F 74 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG F 74 " occ=0.49 Time building chain proxies: 5.28, per 1000 atoms: 0.37 Number of scatterers: 14253 At special positions: 0 Unit cell: (92.66, 133.25, 129.97, 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) S 71 16.00 P 18 15.00 Mg 6 11.99 O 2741 8.00 N 2418 7.00 C 8999 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: 1.31 Conformation dependent library (CDL) restraints added in 998.2 milliseconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 6 sheets defined 60.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 51 through 61 removed outlier: 3.509A pdb=" N LYS A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.532A pdb=" N ALA A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 66 " --> pdb=" O ALA A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.727A pdb=" N SER A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.638A pdb=" N ILE A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 113 removed outlier: 4.972A pdb=" N TYR A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.644A pdb=" N SER A 118 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN A 119 " --> pdb=" O VAL A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 119' Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.844A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.615A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 317 removed outlier: 3.787A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 4.344A pdb=" N LYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 42 removed outlier: 3.562A pdb=" N LYS B 42 " --> pdb=" O LEU B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.508A pdb=" N LEU B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.938A pdb=" N GLU B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.561A pdb=" N LEU B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.536A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.286A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.642A pdb=" N TYR B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.626A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 61 Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.926A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.531A pdb=" N THR C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 76 " --> pdb=" O TYR C 72 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.563A pdb=" N LEU C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.849A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.734A pdb=" N SER C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.210A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.551A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 310 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 340 through 346 removed outlier: 3.766A pdb=" N PHE C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 61 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 70 through 77 removed outlier: 3.638A pdb=" N ILE D 76 " --> pdb=" O TYR D 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.743A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.386A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.545A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 340 through 347 removed outlier: 3.991A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 70 through 77 removed outlier: 3.538A pdb=" N THR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.503A pdb=" N SER E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.297A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 3.518A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 310 Processing helix chain 'E' and resid 310 through 320 Processing helix chain 'E' and resid 340 through 347 removed outlier: 3.778A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.507A pdb=" N ALA F 65 " --> pdb=" O PRO F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 70 through 77 Processing helix chain 'F' and resid 89 through 93 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 206 through 222 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 242 through 247 removed outlier: 3.527A pdb=" N ARG F 247 " --> pdb=" O ASP F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 282 through 290 removed outlier: 3.813A pdb=" N ILE F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 310 Processing helix chain 'F' and resid 310 through 319 removed outlier: 3.561A pdb=" N GLN F 319 " --> pdb=" O LYS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 4.162A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.754A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP A 192 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 230 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.928A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 234 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 4.108A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP C 192 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 234 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 129 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR C 235 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU C 131 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.967A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY D 128 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE D 253 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU D 130 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 removed outlier: 4.093A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE E 190 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP E 192 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR E 235 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 removed outlier: 4.220A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1971 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: 2.54 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4616 1.35 - 1.47: 3003 1.47 - 1.58: 6725 1.58 - 1.70: 20 1.70 - 1.82: 124 Bond restraints: 14488 Sorted by residual: bond pdb=" N SER A 150 " pdb=" CA SER A 150 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.25e-02 6.40e+03 6.03e+00 bond pdb=" CB GLU C 45 " pdb=" CG GLU C 45 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" CB LYS E 342 " pdb=" CG LYS E 342 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CB GLN B 91 " pdb=" CG GLN B 91 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" CA SER A 150 " pdb=" CB SER A 150 " ideal model delta sigma weight residual 1.527 1.507 0.020 1.44e-02 4.82e+03 1.95e+00 ... (remaining 14483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 19242 2.12 - 4.24: 261 4.24 - 6.37: 50 6.37 - 8.49: 11 8.49 - 10.61: 7 Bond angle restraints: 19571 Sorted by residual: angle pdb=" CB LYS E 342 " pdb=" CG LYS E 342 " pdb=" CD LYS E 342 " ideal model delta sigma weight residual 111.30 121.91 -10.61 2.30e+00 1.89e-01 2.13e+01 angle pdb=" CB LYS E 59 " pdb=" CG LYS E 59 " pdb=" CD LYS E 59 " ideal model delta sigma weight residual 111.30 120.08 -8.78 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CA GLU C 45 " pdb=" CB GLU C 45 " pdb=" CG GLU C 45 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CB ILE F 157 " pdb=" CG1 ILE F 157 " pdb=" CD1 ILE F 157 " ideal model delta sigma weight residual 113.80 121.71 -7.91 2.10e+00 2.27e-01 1.42e+01 angle pdb=" CA ILE F 157 " pdb=" CB ILE F 157 " pdb=" CG1 ILE F 157 " ideal model delta sigma weight residual 110.40 116.43 -6.03 1.70e+00 3.46e-01 1.26e+01 ... (remaining 19566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 7324 17.73 - 35.45: 1253 35.45 - 53.18: 408 53.18 - 70.90: 99 70.90 - 88.63: 25 Dihedral angle restraints: 9109 sinusoidal: 3895 harmonic: 5214 Sorted by residual: dihedral pdb=" CA LEU B 184 " pdb=" C LEU B 184 " pdb=" N GLN B 185 " pdb=" CA GLN B 185 " ideal model delta harmonic sigma weight residual -180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU D 184 " pdb=" C LEU D 184 " pdb=" N GLN D 185 " pdb=" CA GLN D 185 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU C 223 " pdb=" C LEU C 223 " pdb=" N LEU C 224 " pdb=" CA LEU C 224 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 9106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1604 0.038 - 0.075: 432 0.075 - 0.113: 164 0.113 - 0.150: 34 0.150 - 0.188: 3 Chirality restraints: 2237 Sorted by residual: chirality pdb=" CB ILE F 157 " pdb=" CA ILE F 157 " pdb=" CG1 ILE F 157 " pdb=" CG2 ILE F 157 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CB ILE D 157 " pdb=" CA ILE D 157 " pdb=" CG1 ILE D 157 " pdb=" CG2 ILE D 157 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CG LEU F 348 " pdb=" CB LEU F 348 " pdb=" CD1 LEU F 348 " pdb=" CD2 LEU F 348 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 2234 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 97 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO E 98 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 104 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C HIS A 104 " 0.027 2.00e-02 2.50e+03 pdb=" O HIS A 104 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU A 105 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 82 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO E 83 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 83 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 83 " 0.021 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 141 2.58 - 3.16: 11254 3.16 - 3.74: 24411 3.74 - 4.32: 33945 4.32 - 4.90: 55063 Nonbonded interactions: 124814 Sorted by model distance: nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 402 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR C 140 " pdb="MG MG C 402 " model vdw 2.008 2.170 nonbonded pdb=" OG1 THR F 140 " pdb="MG MG F 402 " model vdw 2.015 2.170 nonbonded pdb=" OG1 THR E 140 " pdb="MG MG E 402 " model vdw 2.020 2.170 nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 2.024 2.170 ... (remaining 124809 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 50 through 73 or resid 75 through 402)) selection = (chain 'B' and (resid 50 through 73 or resid 75 through 317 or resid 338 through \ 349 or resid 401 through 402)) selection = (chain 'C' and (resid 50 through 73 or resid 75 through 317 or resid 338 through \ 349 or resid 401 through 402)) selection = (chain 'D' and (resid 50 through 73 or resid 75 through 317 or resid 338 through \ 349 or resid 401 through 402)) selection = (chain 'E' and (resid 50 through 73 or resid 75 through 317 or resid 338 through \ 349 or resid 401 through 402)) selection = (chain 'F' and (resid 50 through 73 or resid 75 through 317 or resid 338 through \ 349 or resid 401 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.760 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: 0.860 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.980 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.003 0.050 14488 Z= 0.149 Angle : 0.653 10.612 19571 Z= 0.324 Chirality : 0.042 0.188 2237 Planarity : 0.005 0.055 2455 Dihedral : 20.159 88.629 5715 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 2.75 % Allowed : 33.95 % Favored : 63.30 % 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: -0.44 (0.19), residues: 1757 helix: -0.40 (0.15), residues: 962 sheet: -1.06 (0.39), residues: 175 loop : 0.54 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 199 TYR 0.008 0.001 TYR D 313 PHE 0.020 0.001 PHE B 197 TRP 0.006 0.001 TRP D 166 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00327 (14488) covalent geometry : angle 0.65324 (19571) hydrogen bonds : bond 0.21547 ( 680) hydrogen bonds : angle 6.92600 ( 1971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7983 (pmm-80) cc_final: 0.7755 (pmm-80) REVERT: B 261 ASP cc_start: 0.7660 (t0) cc_final: 0.7428 (t0) REVERT: E 59 LYS cc_start: 0.7889 (tppt) cc_final: 0.7628 (tttp) REVERT: E 92 ASP cc_start: 0.8085 (m-30) cc_final: 0.7802 (m-30) REVERT: E 342 LYS cc_start: 0.7854 (tppt) cc_final: 0.7172 (ttpt) outliers start: 39 outliers final: 36 residues processed: 241 average time/residue: 0.5702 time to fit residues: 152.3192 Evaluate side-chains 246 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN C 104 HIS C 262 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.156639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105293 restraints weight = 50402.639| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.32 r_work: 0.2802 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 14488 Z= 0.282 Angle : 0.643 8.745 19571 Z= 0.318 Chirality : 0.045 0.168 2237 Planarity : 0.005 0.056 2455 Dihedral : 12.454 82.883 2180 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 4.09 % Allowed : 30.69 % Favored : 65.22 % 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: 0.48 (0.20), residues: 1757 helix: 0.64 (0.16), residues: 958 sheet: -1.36 (0.36), residues: 190 loop : 0.70 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 263 TYR 0.011 0.001 TYR E 132 PHE 0.010 0.002 PHE C 154 TRP 0.013 0.002 TRP D 220 HIS 0.004 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00684 (14488) covalent geometry : angle 0.64338 (19571) hydrogen bonds : bond 0.04545 ( 680) hydrogen bonds : angle 4.67359 ( 1971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 154 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7780 (t80) REVERT: E 59 LYS cc_start: 0.7943 (tppt) cc_final: 0.7620 (tttp) REVERT: E 308 ASP cc_start: 0.8205 (t0) cc_final: 0.7758 (OUTLIER) REVERT: E 342 LYS cc_start: 0.7849 (tppt) cc_final: 0.7111 (ttpt) REVERT: F 113 MET cc_start: 0.6692 (pmm) cc_final: 0.6025 (pmt) REVERT: F 284 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7260 (tp-100) outliers start: 60 outliers final: 29 residues processed: 252 average time/residue: 0.5770 time to fit residues: 160.9490 Evaluate side-chains 230 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 262 GLN E 289 ASN F 193 GLN F 289 ASN F 319 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.160157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107075 restraints weight = 43752.356| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.37 r_work: 0.2838 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14488 Z= 0.156 Angle : 0.545 6.768 19571 Z= 0.271 Chirality : 0.041 0.159 2237 Planarity : 0.004 0.035 2455 Dihedral : 11.870 94.643 2140 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 3.90 % Allowed : 31.07 % Favored : 65.03 % 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: 1.02 (0.20), residues: 1757 helix: 1.15 (0.17), residues: 951 sheet: -1.22 (0.36), residues: 182 loop : 0.80 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.008 0.001 TYR F 132 PHE 0.008 0.001 PHE D 245 TRP 0.007 0.001 TRP D 220 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00371 (14488) covalent geometry : angle 0.54502 (19571) hydrogen bonds : bond 0.03655 ( 680) hydrogen bonds : angle 4.44516 ( 1971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8492 (mm-30) REVERT: A 298 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5381 (mp) REVERT: C 74 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6365 (mtm-85) REVERT: E 308 ASP cc_start: 0.8216 (t0) cc_final: 0.7805 (OUTLIER) REVERT: E 342 LYS cc_start: 0.7810 (tppt) cc_final: 0.7134 (ttpt) REVERT: E 350 MET cc_start: 0.6504 (mmt) cc_final: 0.6062 (mmt) REVERT: F 113 MET cc_start: 0.6687 (pmm) cc_final: 0.5863 (pmt) REVERT: F 213 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5723 (mmtm) REVERT: F 284 GLN cc_start: 0.7501 (tp-100) cc_final: 0.7053 (tp-100) outliers start: 57 outliers final: 19 residues processed: 254 average time/residue: 0.5895 time to fit residues: 165.5785 Evaluate side-chains 227 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 151 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 262 GLN F 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126187 restraints weight = 47532.605| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 6.83 r_work: 0.2750 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14488 Z= 0.110 Angle : 0.515 6.955 19571 Z= 0.257 Chirality : 0.040 0.147 2237 Planarity : 0.004 0.076 2455 Dihedral : 11.346 74.720 2134 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 3.39 % Allowed : 31.65 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.34 (0.21), residues: 1757 helix: 1.47 (0.17), residues: 951 sheet: -1.25 (0.38), residues: 162 loop : 0.81 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 263 TYR 0.007 0.001 TYR F 132 PHE 0.024 0.001 PHE F 197 TRP 0.005 0.001 TRP D 166 HIS 0.002 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00250 (14488) covalent geometry : angle 0.51526 (19571) hydrogen bonds : bond 0.03140 ( 680) hydrogen bonds : angle 4.26727 ( 1971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8691 (mm-30) REVERT: B 91 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8003 (mm-40) REVERT: C 74 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6306 (mtm-85) REVERT: E 59 LYS cc_start: 0.7873 (tppt) cc_final: 0.7587 (tttp) REVERT: E 308 ASP cc_start: 0.8274 (t0) cc_final: 0.7850 (OUTLIER) REVERT: E 342 LYS cc_start: 0.7757 (tppt) cc_final: 0.7099 (ttpt) REVERT: E 350 MET cc_start: 0.6700 (mmt) cc_final: 0.6407 (mmp) REVERT: F 113 MET cc_start: 0.6588 (pmm) cc_final: 0.5758 (pmt) REVERT: F 213 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5932 (mmtm) REVERT: F 284 GLN cc_start: 0.7404 (tp-100) cc_final: 0.6859 (tp-100) outliers start: 49 outliers final: 23 residues processed: 250 average time/residue: 0.5887 time to fit residues: 162.2009 Evaluate side-chains 230 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 36 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 109 optimal weight: 0.3980 chunk 122 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 149 optimal weight: 0.0570 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 262 GLN D 316 GLN F 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111648 restraints weight = 38310.878| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.86 r_work: 0.2921 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14488 Z= 0.111 Angle : 0.506 6.603 19571 Z= 0.251 Chirality : 0.040 0.143 2237 Planarity : 0.003 0.051 2455 Dihedral : 11.350 93.408 2129 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 3.07 % Allowed : 32.16 % Favored : 64.77 % 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: 1.51 (0.21), residues: 1757 helix: 1.61 (0.17), residues: 951 sheet: -1.16 (0.38), residues: 162 loop : 0.89 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 263 TYR 0.011 0.001 TYR C 264 PHE 0.006 0.001 PHE D 154 TRP 0.005 0.001 TRP D 166 HIS 0.002 0.000 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00253 (14488) covalent geometry : angle 0.50610 (19571) hydrogen bonds : bond 0.03043 ( 680) hydrogen bonds : angle 4.14531 ( 1971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 298 LEU cc_start: 0.5591 (OUTLIER) cc_final: 0.5367 (mp) REVERT: B 91 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7923 (mm-40) REVERT: B 261 ASP cc_start: 0.7618 (t0) cc_final: 0.7170 (t0) REVERT: C 74 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6192 (mtm-85) REVERT: C 288 ASP cc_start: 0.7711 (m-30) cc_final: 0.7005 (m-30) REVERT: E 179 SER cc_start: 0.8380 (t) cc_final: 0.8116 (p) REVERT: E 308 ASP cc_start: 0.8140 (t0) cc_final: 0.7722 (OUTLIER) REVERT: E 342 LYS cc_start: 0.7801 (tppt) cc_final: 0.7158 (ttpt) REVERT: F 113 MET cc_start: 0.6737 (pmm) cc_final: 0.5870 (pmt) REVERT: F 149 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7127 (tt0) REVERT: F 213 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5924 (tptt) REVERT: F 284 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7013 (tp-100) REVERT: F 288 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7842 (m-30) outliers start: 44 outliers final: 20 residues processed: 240 average time/residue: 0.5894 time to fit residues: 155.9497 Evaluate side-chains 230 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 25 optimal weight: 9.9990 chunk 97 optimal weight: 0.2980 chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 262 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN F 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.160906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110718 restraints weight = 49052.681| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.14 r_work: 0.2871 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14488 Z= 0.183 Angle : 0.565 8.373 19571 Z= 0.278 Chirality : 0.042 0.163 2237 Planarity : 0.004 0.047 2455 Dihedral : 11.487 89.205 2129 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 3.58 % Allowed : 32.03 % Favored : 64.39 % 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 (0.21), residues: 1757 helix: 1.55 (0.17), residues: 949 sheet: -1.18 (0.37), residues: 179 loop : 1.03 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 263 TYR 0.007 0.001 TYR E 132 PHE 0.009 0.001 PHE D 154 TRP 0.009 0.001 TRP C 220 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00443 (14488) covalent geometry : angle 0.56475 (19571) hydrogen bonds : bond 0.03325 ( 680) hydrogen bonds : angle 4.22807 ( 1971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8328 (mm-30) REVERT: A 298 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5454 (mp) REVERT: B 261 ASP cc_start: 0.7626 (t0) cc_final: 0.7178 (t0) REVERT: C 74 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6365 (mtm-85) REVERT: E 59 LYS cc_start: 0.7961 (tppt) cc_final: 0.7669 (tttp) REVERT: E 308 ASP cc_start: 0.8235 (t0) cc_final: 0.7855 (OUTLIER) REVERT: F 113 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.5812 (pmt) REVERT: F 213 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.6072 (tptt) REVERT: F 284 GLN cc_start: 0.7500 (tp-100) cc_final: 0.7205 (tm-30) REVERT: F 288 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7805 (m-30) outliers start: 52 outliers final: 22 residues processed: 247 average time/residue: 0.5787 time to fit residues: 158.1263 Evaluate side-chains 237 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 41 optimal weight: 4.9990 chunk 170 optimal weight: 0.0030 chunk 163 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 155 optimal weight: 0.0970 chunk 137 optimal weight: 2.9990 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 262 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN F 236 ASN F 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.111056 restraints weight = 52917.402| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.32 r_work: 0.2836 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14488 Z= 0.172 Angle : 0.565 10.660 19571 Z= 0.277 Chirality : 0.042 0.163 2237 Planarity : 0.004 0.053 2455 Dihedral : 11.313 77.511 2129 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 3.45 % Allowed : 32.10 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.21), residues: 1757 helix: 1.55 (0.17), residues: 951 sheet: -1.26 (0.38), residues: 167 loop : 1.02 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.009 0.001 TYR F 132 PHE 0.025 0.001 PHE F 197 TRP 0.007 0.001 TRP D 220 HIS 0.004 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00415 (14488) covalent geometry : angle 0.56510 (19571) hydrogen bonds : bond 0.03272 ( 680) hydrogen bonds : angle 4.22750 ( 1971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7302 (ttp80) REVERT: B 91 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8016 (mm-40) REVERT: B 261 ASP cc_start: 0.7629 (t0) cc_final: 0.7171 (t0) REVERT: C 74 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6264 (mtm-85) REVERT: C 288 ASP cc_start: 0.7784 (m-30) cc_final: 0.7087 (m-30) REVERT: E 59 LYS cc_start: 0.7910 (tppt) cc_final: 0.7612 (tttp) REVERT: E 308 ASP cc_start: 0.8220 (t0) cc_final: 0.7849 (OUTLIER) REVERT: F 113 MET cc_start: 0.6672 (pmm) cc_final: 0.5937 (pmm) REVERT: F 213 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.6023 (tptt) REVERT: F 284 GLN cc_start: 0.7403 (tp-100) cc_final: 0.7134 (tm-30) REVERT: F 288 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7791 (m-30) outliers start: 51 outliers final: 25 residues processed: 241 average time/residue: 0.5808 time to fit residues: 154.9106 Evaluate side-chains 234 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 342 LYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 53 GLN C 262 GLN F 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123134 restraints weight = 53725.524| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 6.80 r_work: 0.2850 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14488 Z= 0.115 Angle : 0.523 10.965 19571 Z= 0.259 Chirality : 0.041 0.181 2237 Planarity : 0.003 0.048 2455 Dihedral : 11.169 78.633 2129 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 2.75 % Allowed : 32.86 % Favored : 64.39 % 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: 1.70 (0.21), residues: 1757 helix: 1.70 (0.17), residues: 953 sheet: -1.04 (0.39), residues: 153 loop : 1.03 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.009 0.001 TYR F 132 PHE 0.007 0.001 PHE F 281 TRP 0.006 0.001 TRP D 166 HIS 0.003 0.000 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00268 (14488) covalent geometry : angle 0.52271 (19571) hydrogen bonds : bond 0.02944 ( 680) hydrogen bonds : angle 4.13501 ( 1971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 205 ASP cc_start: 0.8025 (m-30) cc_final: 0.7794 (m-30) REVERT: A 261 ASP cc_start: 0.7399 (t0) cc_final: 0.6726 (t0) REVERT: A 265 LYS cc_start: 0.6651 (mttt) cc_final: 0.6347 (mttt) REVERT: B 91 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8103 (mm-40) REVERT: B 261 ASP cc_start: 0.7657 (t0) cc_final: 0.7181 (t0) REVERT: C 74 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6452 (mtm-85) REVERT: C 205 ASP cc_start: 0.8552 (t0) cc_final: 0.8347 (t0) REVERT: E 59 LYS cc_start: 0.7920 (tppt) cc_final: 0.7617 (tttp) REVERT: E 284 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7682 (tm-30) REVERT: E 308 ASP cc_start: 0.8322 (t0) cc_final: 0.7919 (t0) REVERT: F 112 MET cc_start: 0.7287 (mmm) cc_final: 0.7084 (mpm) REVERT: F 213 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5771 (mmtm) REVERT: F 279 ASP cc_start: 0.6614 (OUTLIER) cc_final: 0.5529 (t0) REVERT: F 284 GLN cc_start: 0.7421 (tp-100) cc_final: 0.7145 (tm-30) REVERT: F 288 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7856 (m-30) outliers start: 40 outliers final: 21 residues processed: 236 average time/residue: 0.5896 time to fit residues: 153.7330 Evaluate side-chains 234 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 168 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 53 GLN C 262 GLN F 236 ASN F 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120192 restraints weight = 44119.485| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 6.48 r_work: 0.2893 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14488 Z= 0.138 Angle : 0.537 10.637 19571 Z= 0.266 Chirality : 0.041 0.156 2237 Planarity : 0.004 0.045 2455 Dihedral : 11.176 79.034 2129 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 2.75 % Allowed : 32.86 % Favored : 64.39 % 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: 1.71 (0.21), residues: 1757 helix: 1.74 (0.17), residues: 953 sheet: -1.08 (0.39), residues: 154 loop : 1.02 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.012 0.001 TYR C 264 PHE 0.023 0.001 PHE F 197 TRP 0.006 0.001 TRP E 166 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00329 (14488) covalent geometry : angle 0.53727 (19571) hydrogen bonds : bond 0.03025 ( 680) hydrogen bonds : angle 4.11588 ( 1971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 199 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7443 (ttp80) REVERT: A 261 ASP cc_start: 0.7417 (t0) cc_final: 0.6692 (t0) REVERT: A 265 LYS cc_start: 0.6709 (mttt) cc_final: 0.6378 (mttt) REVERT: B 91 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8117 (mm-40) REVERT: B 261 ASP cc_start: 0.7657 (t0) cc_final: 0.7176 (t0) REVERT: C 74 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6508 (mtm-85) REVERT: C 205 ASP cc_start: 0.8582 (t0) cc_final: 0.8345 (t0) REVERT: C 284 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: C 288 ASP cc_start: 0.7916 (m-30) cc_final: 0.7056 (m-30) REVERT: E 59 LYS cc_start: 0.7931 (tppt) cc_final: 0.7636 (tttp) REVERT: E 308 ASP cc_start: 0.8333 (t0) cc_final: 0.7943 (t0) REVERT: F 213 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.6059 (tptt) REVERT: F 279 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.5429 (t0) REVERT: F 284 GLN cc_start: 0.7470 (tp-100) cc_final: 0.7203 (tm-30) REVERT: F 288 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7865 (m-30) outliers start: 40 outliers final: 21 residues processed: 234 average time/residue: 0.5903 time to fit residues: 152.4384 Evaluate side-chains 234 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 143 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 262 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN F 193 GLN F 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.163760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119644 restraints weight = 42497.367| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 6.38 r_work: 0.2903 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14488 Z= 0.136 Angle : 0.549 10.571 19571 Z= 0.269 Chirality : 0.041 0.168 2237 Planarity : 0.003 0.034 2455 Dihedral : 11.116 80.323 2129 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 2.56 % Allowed : 33.31 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.21), residues: 1757 helix: 1.72 (0.17), residues: 953 sheet: -1.07 (0.39), residues: 154 loop : 1.03 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 263 TYR 0.009 0.001 TYR B 264 PHE 0.007 0.001 PHE D 154 TRP 0.006 0.001 TRP D 166 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00323 (14488) covalent geometry : angle 0.54865 (19571) hydrogen bonds : bond 0.03027 ( 680) hydrogen bonds : angle 4.12620 ( 1971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7446 (ttp80) REVERT: A 215 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: B 91 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8072 (mm-40) REVERT: B 261 ASP cc_start: 0.7626 (t0) cc_final: 0.7143 (t0) REVERT: C 74 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6468 (mtm-85) REVERT: C 205 ASP cc_start: 0.8579 (t0) cc_final: 0.8334 (t0) REVERT: C 284 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6514 (tm-30) REVERT: C 288 ASP cc_start: 0.7913 (m-30) cc_final: 0.7042 (m-30) REVERT: E 59 LYS cc_start: 0.7938 (tppt) cc_final: 0.7631 (tttp) REVERT: E 124 GLN cc_start: 0.8446 (mt0) cc_final: 0.8181 (mm110) REVERT: E 284 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7724 (tm-30) REVERT: E 308 ASP cc_start: 0.8326 (t0) cc_final: 0.7944 (t0) REVERT: E 350 MET cc_start: 0.6649 (mmm) cc_final: 0.4771 (tmm) REVERT: F 213 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.6036 (tptt) REVERT: F 284 GLN cc_start: 0.7467 (tp-100) cc_final: 0.7193 (tm-30) REVERT: F 288 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7836 (m-30) outliers start: 37 outliers final: 21 residues processed: 230 average time/residue: 0.5479 time to fit residues: 139.4355 Evaluate side-chains 233 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 213 LYS Chi-restraints excluded: chain F residue 279 ASP Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 70 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 170 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 119 ASN C 262 GLN ** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN F 236 ASN F 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.165792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121773 restraints weight = 45235.704| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 6.59 r_work: 0.2928 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14488 Z= 0.111 Angle : 0.522 10.323 19571 Z= 0.258 Chirality : 0.041 0.154 2237 Planarity : 0.003 0.051 2455 Dihedral : 10.995 80.096 2129 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 2.11 % Allowed : 33.82 % Favored : 64.07 % 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: 1.79 (0.21), residues: 1757 helix: 1.84 (0.17), residues: 953 sheet: -1.13 (0.39), residues: 152 loop : 1.01 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.006 0.001 TYR F 132 PHE 0.006 0.001 PHE D 154 TRP 0.005 0.001 TRP D 166 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00257 (14488) covalent geometry : angle 0.52235 (19571) hydrogen bonds : bond 0.02855 ( 680) hydrogen bonds : angle 4.05260 ( 1971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7089.95 seconds wall clock time: 121 minutes 37.40 seconds (7297.40 seconds total)