Starting phenix.real_space_refine on Sun Sep 13 03:03:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f0x_4166/09_2026/6f0x_4166_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f0x_4166/09_2026/6f0x_4166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6f0x_4166/09_2026/6f0x_4166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f0x_4166/09_2026/6f0x_4166.map" model { file = "/net/cci-nas-00/data/ceres_data/6f0x_4166/09_2026/6f0x_4166_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f0x_4166/09_2026/6f0x_4166_neut.cif" } resolution = 4.6 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= 0.003 sd= 0.017 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 69 5.16 5 C 13043 2.51 5 N 3511 2.21 5 O 3812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20450 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2410 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 298} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3097 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3077 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3118 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3071 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2241 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1563 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Chain breaks: 3 Chain: "Q" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "Z" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1648 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.10, per 1000 atoms: 0.20 Number of scatterers: 20450 At special positions: 0 Unit cell: (145.86, 144.43, 147.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 15 15.00 O 3812 8.00 N 3511 7.00 C 13043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Z 79 " - pdb=" SG CYS Z 106 " distance=2.03 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 Atom "HETATM20319 O3B AGS A 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 776.0 milliseconds 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4978 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 20 sheets defined 49.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.313A pdb=" N SER A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 221 through 241 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 323 through 341 Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 384 through 398 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 408 through 428 removed outlier: 3.561A pdb=" N GLN A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.650A pdb=" N SER B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 163 removed outlier: 3.748A pdb=" N VAL B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 200 Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.599A pdb=" N PHE B 218 " --> pdb=" O HIS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 242 removed outlier: 3.696A pdb=" N LYS B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.960A pdb=" N ASN B 262 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 288 removed outlier: 4.587A pdb=" N ALA B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.091A pdb=" N ASP B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 341 Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 384 through 399 Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 406 through 429 removed outlier: 3.652A pdb=" N PHE B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.752A pdb=" N PHE C 132 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.056A pdb=" N VAL C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 213 through 218 removed outlier: 4.053A pdb=" N PHE C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 242 removed outlier: 3.687A pdb=" N LYS C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 269 through 288 removed outlier: 4.495A pdb=" N ARG C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 306 through 313 removed outlier: 4.132A pdb=" N VAL C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 341 Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 364 through 381 removed outlier: 3.920A pdb=" N LEU C 369 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 399 Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 409 through 428 Processing helix chain 'D' and resid 34 through 50 removed outlier: 3.744A pdb=" N ILE D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 144 through 159 removed outlier: 4.118A pdb=" N HIS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 157 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 200 Processing helix chain 'D' and resid 214 through 217 Processing helix chain 'D' and resid 223 through 242 removed outlier: 4.327A pdb=" N LYS D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 267 through 288 removed outlier: 4.489A pdb=" N ALA D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 341 Processing helix chain 'D' and resid 352 through 359 removed outlier: 3.718A pdb=" N ILE D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 381 Processing helix chain 'D' and resid 384 through 400 Proline residue: D 392 - end of helix removed outlier: 3.637A pdb=" N VAL D 400 " --> pdb=" O HIS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 429 removed outlier: 3.813A pdb=" N ALA D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 50 removed outlier: 3.515A pdb=" N ILE E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.727A pdb=" N PHE E 132 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.840A pdb=" N LEU E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 163 removed outlier: 3.847A pdb=" N HIS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 201 Processing helix chain 'E' and resid 225 through 241 removed outlier: 4.135A pdb=" N ASP E 241 " --> pdb=" O GLN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 270 through 287 Processing helix chain 'E' and resid 288 through 290 No H-bonds generated for 'chain 'E' and resid 288 through 290' Processing helix chain 'E' and resid 323 through 341 Processing helix chain 'E' and resid 352 through 359 Processing helix chain 'E' and resid 366 through 379 removed outlier: 4.178A pdb=" N SER E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 389 Processing helix chain 'E' and resid 390 through 400 removed outlier: 4.046A pdb=" N LEU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 428 Processing helix chain 'F' and resid 129 through 133 removed outlier: 4.179A pdb=" N PHE F 132 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 163 removed outlier: 3.709A pdb=" N ASP F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR F 152 " --> pdb=" O HIS F 148 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU F 158 " --> pdb=" O MET F 154 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN F 163 " --> pdb=" O PHE F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 200 Processing helix chain 'F' and resid 228 through 241 Processing helix chain 'F' and resid 254 through 259 removed outlier: 3.838A pdb=" N LEU F 257 " --> pdb=" O VAL F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 306 through 311 removed outlier: 4.162A pdb=" N VAL F 310 " --> pdb=" O ASP F 306 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 306 through 311' Processing helix chain 'F' and resid 323 through 339 Processing helix chain 'F' and resid 352 through 359 Processing helix chain 'F' and resid 367 through 379 removed outlier: 4.193A pdb=" N LEU F 371 " --> pdb=" O SER F 367 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS F 379 " --> pdb=" O ASP F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 399 Proline residue: F 392 - end of helix Processing helix chain 'F' and resid 406 through 424 removed outlier: 3.550A pdb=" N PHE F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 84 removed outlier: 3.740A pdb=" N GLN P 71 " --> pdb=" O GLU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 145 Processing helix chain 'P' and resid 182 through 197 Processing helix chain 'P' and resid 254 through 259 removed outlier: 3.753A pdb=" N ASP P 259 " --> pdb=" O THR P 255 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 35 Processing helix chain 'Z' and resid 58 through 78 Processing helix chain 'Z' and resid 107 through 112 Processing helix chain 'Z' and resid 120 through 139 removed outlier: 3.686A pdb=" N VAL Z 139 " --> pdb=" O ILE Z 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 126 removed outlier: 6.605A pdb=" N TYR A 206 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE A 248 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN A 208 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU A 250 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 210 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU A 296 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 249 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR A 298 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 251 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLN A 317 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 176 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 58 removed outlier: 4.090A pdb=" N SER B 72 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 74 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 24 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 23 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE B 100 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 25 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 126 removed outlier: 7.425A pdb=" N GLN B 208 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU B 250 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 210 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASP B 252 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ILE B 212 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL B 247 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 296 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL B 249 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR B 298 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 251 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL B 174 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLN B 317 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 176 " --> pdb=" O GLN B 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 20 through 22 Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AA6, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 126 removed outlier: 3.579A pdb=" N ASN C 123 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL C 175 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 20 through 22 Processing sheet with id=AA9, first strand: chain 'D' and resid 57 through 58 removed outlier: 4.380A pdb=" N SER D 72 " --> pdb=" O HIS D 26 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS D 26 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 74 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL D 25 " --> pdb=" O PHE D 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 122 through 126 removed outlier: 4.430A pdb=" N ILE D 212 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE D 315 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 26 through 27 Processing sheet with id=AB3, first strand: chain 'E' and resid 123 through 126 removed outlier: 6.566A pdb=" N VAL E 175 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 123 through 126 removed outlier: 5.655A pdb=" N VAL F 249 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 123 through 126 removed outlier: 7.667A pdb=" N TYR F 206 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 177 through 178 removed outlier: 3.606A pdb=" N HIS F 178 " --> pdb=" O GLN F 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'P' and resid 227 through 228 removed outlier: 3.778A pdb=" N ALA P 215 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG P 149 " --> pdb=" O GLN P 216 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE P 164 " --> pdb=" O LEU P 241 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL P 243 " --> pdb=" O PHE P 164 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU P 166 " --> pdb=" O VAL P 243 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 227 through 228 removed outlier: 3.778A pdb=" N ALA P 215 " --> pdb=" O PHE P 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 131 through 132 Processing sheet with id=AC1, first strand: chain 'Z' and resid 44 through 48 Processing sheet with id=AC2, first strand: chain 'Z' and resid 149 through 157 removed outlier: 4.806A pdb=" N GLN Z 82 " --> pdb=" O ILE Z 104 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN Z 90 " --> pdb=" O VAL Z 96 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL Z 96 " --> pdb=" O ASN Z 90 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU Z 97 " --> pdb=" O LYS Z 200 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6830 1.36 - 1.51: 6079 1.51 - 1.65: 7801 1.65 - 1.80: 49 1.80 - 1.94: 50 Bond restraints: 20809 Sorted by residual: bond pdb=" O3B AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 1.673 1.548 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" O3B AGS C 901 " pdb=" PB AGS C 901 " ideal model delta sigma weight residual 1.673 1.556 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" O3A AGS B 901 " pdb=" PA AGS B 901 " ideal model delta sigma weight residual 1.664 1.548 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O3B AGS B 901 " pdb=" PB AGS B 901 " ideal model delta sigma weight residual 1.673 1.558 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" O3A AGS D 901 " pdb=" PA AGS D 901 " ideal model delta sigma weight residual 1.664 1.554 0.110 2.00e-02 2.50e+03 3.03e+01 ... (remaining 20804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 27752 3.15 - 6.30: 405 6.30 - 9.45: 67 9.45 - 12.60: 16 12.60 - 15.75: 4 Bond angle restraints: 28244 Sorted by residual: angle pdb=" PB AGS B 901 " pdb=" O3B AGS B 901 " pdb=" PG AGS B 901 " ideal model delta sigma weight residual 129.21 113.46 15.75 3.00e+00 1.11e-01 2.76e+01 angle pdb=" CA ALA C 130 " pdb=" C ALA C 130 " pdb=" O ALA C 130 " ideal model delta sigma weight residual 120.51 113.28 7.23 1.43e+00 4.89e-01 2.55e+01 angle pdb=" N GLU D 269 " pdb=" CA GLU D 269 " pdb=" C GLU D 269 " ideal model delta sigma weight residual 113.45 106.48 6.97 1.39e+00 5.18e-01 2.51e+01 angle pdb=" PB AGS C 901 " pdb=" O3B AGS C 901 " pdb=" PG AGS C 901 " ideal model delta sigma weight residual 129.21 114.29 14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" PA AGS A 901 " pdb=" O3A AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 127.08 112.82 14.26 3.00e+00 1.11e-01 2.26e+01 ... (remaining 28239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 12523 35.47 - 70.94: 136 70.94 - 106.40: 36 106.40 - 141.87: 5 141.87 - 177.34: 4 Dihedral angle restraints: 12704 sinusoidal: 5096 harmonic: 7608 Sorted by residual: dihedral pdb=" CA LEU D 127 " pdb=" C LEU D 127 " pdb=" N PRO D 128 " pdb=" CA PRO D 128 " ideal model delta harmonic sigma weight residual -180.00 -123.13 -56.87 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LEU C 127 " pdb=" C LEU C 127 " pdb=" N PRO C 128 " pdb=" CA PRO C 128 " ideal model delta harmonic sigma weight residual -180.00 -124.97 -55.03 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA LEU F 127 " pdb=" C LEU F 127 " pdb=" N PRO F 128 " pdb=" CA PRO F 128 " ideal model delta harmonic sigma weight residual -180.00 -125.94 -54.06 0 5.00e+00 4.00e-02 1.17e+02 ... (remaining 12701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2706 0.065 - 0.129: 591 0.129 - 0.194: 52 0.194 - 0.258: 5 0.258 - 0.323: 5 Chirality restraints: 3359 Sorted by residual: chirality pdb=" C3' AGS C 901 " pdb=" C2' AGS C 901 " pdb=" C4' AGS C 901 " pdb=" O3' AGS C 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.69 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' AGS B 901 " pdb=" C2' AGS B 901 " pdb=" C4' AGS B 901 " pdb=" O3' AGS B 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' AGS D 901 " pdb=" C2' AGS D 901 " pdb=" C4' AGS D 901 " pdb=" O3' AGS D 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3356 not shown) Planarity restraints: 3526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 127 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO D 128 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 127 " 0.063 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO C 128 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 127 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO F 128 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO F 128 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 128 " 0.045 5.00e-02 4.00e+02 ... (remaining 3523 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 265 2.49 - 3.09: 17900 3.09 - 3.69: 31911 3.69 - 4.30: 47014 4.30 - 4.90: 71149 Nonbonded interactions: 168239 Sorted by model distance: nonbonded pdb=" NH1 ARG E 173 " pdb=" O LYS E 288 " model vdw 1.884 3.120 nonbonded pdb=" OE2 GLU B 24 " pdb=" NZ LYS B 195 " model vdw 1.902 3.120 nonbonded pdb=" OE2 GLU F 255 " pdb=" OG SER F 299 " model vdw 1.932 3.040 nonbonded pdb=" OD1 ASN D 103 " pdb=" NZ LYS P 229 " model vdw 1.955 3.120 nonbonded pdb=" OD2 ASP D 244 " pdb=" NH1 ARG P 233 " model vdw 1.983 3.120 ... (remaining 168234 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 122 through 216 or resid 227 through 261 or resid 272 thro \ ugh 345 or resid 347 through 424)) selection = (chain 'F' and (resid 122 through 260 or (resid 261 and (name N or name CA or na \ me C or name O or name CB )) or resid 272 through 305 or (resid 306 through 308 \ and (name N or name CA or name C or name O or name CB )) or resid 309 through 42 \ 4)) } ncs_group { reference = (chain 'B' and (resid 19 through 118 or (resid 119 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 127 or (resid 128 t \ hrough 130 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 214 or (resid 215 and (name N or name CA or name C or name O or name CB \ )) or resid 216 through 261 or (resid 262 through 266 and (name N or name CA or \ name C or name O or name CB )) or (resid 267 through 273 and (name N or name CA \ or name C or name O or name CB )) or resid 274 through 313 or (resid 314 and (n \ ame N or name CA or name C or name O or name CB )) or resid 315 through 424 or ( \ resid 425 through 429 and (name N or name CA or name C or name O or name CB )) o \ r resid 901)) selection = (chain 'C' and (resid 19 through 127 or (resid 128 through 130 and (name N or na \ me CA or name C or name O or name CB )) or resid 131 through 261 or (resid 262 t \ hrough 266 and (name N or name CA or name C or name O or name CB )) or resid 267 \ through 424 or (resid 425 through 429 and (name N or name CA or name C or name \ O or name CB )) or resid 901)) selection = (chain 'D' and (resid 19 through 106 or (resid 107 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 127 or (resid 128 t \ hrough 130 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 261 or (resid 262 through 266 and (name N or name CA or name C or name \ O or name CB )) or resid 267 through 313 or (resid 314 and (name N or name CA or \ name C or name O or name CB )) or resid 315 through 424 or (resid 425 through 4 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'E' and (resid 19 through 119 or (resid 120 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 313 or (resid 314 a \ nd (name N or name CA or name C or name O or name CB )) or resid 315 through 901 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.590 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 0.007 0.125 20823 Z= 0.370 Angle : 1.024 15.753 28246 Z= 0.528 Chirality : 0.052 0.323 3359 Planarity : 0.005 0.105 3526 Dihedral : 12.604 177.338 7723 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.55 % Favored : 81.94 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.20 % 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: -5.29 (0.13), residues: 2541 helix: -3.23 (0.10), residues: 1123 sheet: -3.01 (0.24), residues: 339 loop : -3.89 (0.16), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 265 TYR 0.025 0.003 TYR C 141 PHE 0.030 0.003 PHE C 248 TRP 0.034 0.003 TRP A 221 HIS 0.011 0.002 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.37 (20809) covalent geometry : angle 1.02423 / 0.53 (28244) SS BOND : bond 0.00235 / 0.12 ( 1) SS BOND : angle 0.52215 / 0.35 ( 2) hydrogen bonds : bond 0.16553 / 11.52 ( 961) hydrogen bonds : angle 7.66932 / 5.41 ( 2766) Misc. bond : bond 0.00324 / 0.24 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 896 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TRP cc_start: 0.7815 (m-90) cc_final: 0.7560 (m100) REVERT: A 137 ASP cc_start: 0.8938 (m-30) cc_final: 0.8432 (p0) REVERT: A 168 LEU cc_start: 0.9497 (mt) cc_final: 0.9281 (pt) REVERT: A 173 ARG cc_start: 0.6999 (mtt90) cc_final: 0.6363 (mpt-90) REVERT: A 200 LEU cc_start: 0.9230 (mt) cc_final: 0.8478 (tp) REVERT: A 233 PHE cc_start: 0.7608 (m-80) cc_final: 0.7362 (m-80) REVERT: A 250 LEU cc_start: 0.9672 (tp) cc_final: 0.9417 (tp) REVERT: A 327 ILE cc_start: 0.9475 (mt) cc_final: 0.8181 (mt) REVERT: A 335 LEU cc_start: 0.9518 (mt) cc_final: 0.9289 (mt) REVERT: A 354 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8350 (tmm-80) REVERT: A 358 MET cc_start: 0.8330 (mtm) cc_final: 0.8122 (tmm) REVERT: A 375 ASP cc_start: 0.9389 (m-30) cc_final: 0.8585 (t0) REVERT: A 377 SER cc_start: 0.7557 (m) cc_final: 0.7337 (t) REVERT: A 393 PHE cc_start: 0.9098 (t80) cc_final: 0.8644 (t80) REVERT: A 398 LEU cc_start: 0.9198 (mt) cc_final: 0.8967 (mt) REVERT: A 399 TYR cc_start: 0.8290 (m-80) cc_final: 0.7985 (m-80) REVERT: A 424 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8495 (mt-10) REVERT: B 68 ARG cc_start: 0.9061 (tpt90) cc_final: 0.8755 (tpt90) REVERT: B 105 ASP cc_start: 0.8605 (t0) cc_final: 0.8174 (p0) REVERT: B 135 LEU cc_start: 0.8932 (tp) cc_final: 0.8672 (tp) REVERT: B 146 LYS cc_start: 0.9073 (mtmt) cc_final: 0.8869 (mttp) REVERT: B 188 LEU cc_start: 0.9673 (tp) cc_final: 0.9418 (tp) REVERT: B 189 CYS cc_start: 0.9319 (m) cc_final: 0.9112 (m) REVERT: B 209 LEU cc_start: 0.9296 (tp) cc_final: 0.8729 (tp) REVERT: B 224 GLU cc_start: 0.8110 (tp30) cc_final: 0.7401 (tt0) REVERT: B 231 LYS cc_start: 0.8374 (mttt) cc_final: 0.7864 (tmtt) REVERT: B 244 ASP cc_start: 0.8036 (m-30) cc_final: 0.7635 (m-30) REVERT: B 281 LEU cc_start: 0.9495 (mt) cc_final: 0.8989 (mp) REVERT: B 296 LEU cc_start: 0.9047 (mt) cc_final: 0.8594 (mt) REVERT: B 327 ILE cc_start: 0.9673 (mt) cc_final: 0.9388 (mt) REVERT: B 329 LYS cc_start: 0.9156 (mttt) cc_final: 0.8777 (mtmm) REVERT: B 335 LEU cc_start: 0.9802 (mt) cc_final: 0.9546 (mt) REVERT: B 336 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8761 (mm-30) REVERT: B 339 MET cc_start: 0.8246 (mtt) cc_final: 0.7964 (mmt) REVERT: B 399 TYR cc_start: 0.8851 (m-80) cc_final: 0.8613 (m-80) REVERT: B 408 GLU cc_start: 0.9028 (mp0) cc_final: 0.8738 (tm-30) REVERT: B 419 ASP cc_start: 0.9407 (m-30) cc_final: 0.8994 (m-30) REVERT: C 56 TYR cc_start: 0.6419 (t80) cc_final: 0.6096 (m-80) REVERT: C 58 TRP cc_start: 0.8736 (m-90) cc_final: 0.6818 (m-90) REVERT: C 98 HIS cc_start: 0.6773 (m-70) cc_final: 0.6525 (m-70) REVERT: C 102 LEU cc_start: 0.8945 (mt) cc_final: 0.8714 (mt) REVERT: C 135 LEU cc_start: 0.9488 (tp) cc_final: 0.9069 (tt) REVERT: C 192 LEU cc_start: 0.9702 (tp) cc_final: 0.9395 (tt) REVERT: C 196 LEU cc_start: 0.9592 (mt) cc_final: 0.9355 (mt) REVERT: C 209 LEU cc_start: 0.9208 (tp) cc_final: 0.8985 (tp) REVERT: C 211 GLU cc_start: 0.7446 (tp30) cc_final: 0.6989 (tp30) REVERT: C 224 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7406 (mm-30) REVERT: C 331 TYR cc_start: 0.9107 (m-10) cc_final: 0.8678 (m-10) REVERT: C 383 LEU cc_start: 0.8633 (mt) cc_final: 0.8430 (mt) REVERT: D 27 GLN cc_start: 0.9448 (tt0) cc_final: 0.9236 (tt0) REVERT: D 41 SER cc_start: 0.9348 (m) cc_final: 0.8868 (p) REVERT: D 48 ARG cc_start: 0.8589 (ttm170) cc_final: 0.7997 (mtt180) REVERT: D 66 LEU cc_start: 0.9510 (mt) cc_final: 0.9185 (mp) REVERT: D 108 SER cc_start: 0.9228 (m) cc_final: 0.8957 (t) REVERT: D 135 LEU cc_start: 0.8275 (tp) cc_final: 0.8074 (mp) REVERT: D 136 TRP cc_start: 0.8749 (t-100) cc_final: 0.8527 (t60) REVERT: D 158 LEU cc_start: 0.9101 (tp) cc_final: 0.8537 (tt) REVERT: D 159 PHE cc_start: 0.7510 (m-80) cc_final: 0.6744 (m-80) REVERT: D 165 ASN cc_start: 0.8355 (t0) cc_final: 0.7675 (t0) REVERT: D 171 TRP cc_start: 0.8255 (p-90) cc_final: 0.7150 (p-90) REVERT: D 190 LYS cc_start: 0.9306 (mttt) cc_final: 0.9020 (mtmt) REVERT: D 192 LEU cc_start: 0.9624 (tp) cc_final: 0.9246 (tp) REVERT: D 196 LEU cc_start: 0.9787 (mt) cc_final: 0.9510 (mt) REVERT: D 208 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7844 (mm-40) REVERT: D 209 LEU cc_start: 0.9165 (tp) cc_final: 0.8792 (tp) REVERT: D 211 GLU cc_start: 0.9092 (tt0) cc_final: 0.8642 (tt0) REVERT: D 224 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8436 (tp30) REVERT: D 234 GLN cc_start: 0.9006 (tp40) cc_final: 0.8581 (tm-30) REVERT: D 248 PHE cc_start: 0.9539 (m-80) cc_final: 0.9219 (m-80) REVERT: D 281 LEU cc_start: 0.9309 (mt) cc_final: 0.9098 (mt) REVERT: D 283 GLN cc_start: 0.9498 (mm-40) cc_final: 0.8897 (mm-40) REVERT: D 286 GLN cc_start: 0.8274 (mt0) cc_final: 0.8010 (mt0) REVERT: D 328 PHE cc_start: 0.8949 (t80) cc_final: 0.8745 (t80) REVERT: D 329 LYS cc_start: 0.8935 (mttt) cc_final: 0.8562 (mmtt) REVERT: D 368 LYS cc_start: 0.9451 (tttt) cc_final: 0.9081 (ptmm) REVERT: D 391 LEU cc_start: 0.9553 (mt) cc_final: 0.9240 (mt) REVERT: D 396 HIS cc_start: 0.7845 (t-90) cc_final: 0.7546 (t-90) REVERT: D 423 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8704 (mm-30) REVERT: D 424 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8114 (mt-10) REVERT: E 27 GLN cc_start: 0.7751 (tt0) cc_final: 0.7043 (tt0) REVERT: E 58 TRP cc_start: 0.7376 (m-90) cc_final: 0.6407 (m-90) REVERT: E 62 ASP cc_start: 0.8195 (m-30) cc_final: 0.7703 (t0) REVERT: E 72 SER cc_start: 0.8135 (p) cc_final: 0.7502 (p) REVERT: E 125 TRP cc_start: 0.6709 (m-90) cc_final: 0.6328 (m-10) REVERT: E 148 HIS cc_start: 0.8484 (m170) cc_final: 0.8269 (m90) REVERT: E 154 MET cc_start: 0.8924 (tpt) cc_final: 0.8558 (ttm) REVERT: E 155 THR cc_start: 0.9589 (m) cc_final: 0.9256 (p) REVERT: E 167 ASN cc_start: 0.9572 (m-40) cc_final: 0.9318 (m110) REVERT: E 209 LEU cc_start: 0.8918 (tp) cc_final: 0.8357 (tp) REVERT: E 211 GLU cc_start: 0.7848 (tt0) cc_final: 0.7372 (tm-30) REVERT: E 212 ILE cc_start: 0.7496 (tt) cc_final: 0.7221 (tt) REVERT: E 232 MET cc_start: 0.9250 (ttp) cc_final: 0.9049 (tmm) REVERT: E 254 VAL cc_start: 0.9572 (t) cc_final: 0.9357 (m) REVERT: E 316 LYS cc_start: 0.8365 (mttt) cc_final: 0.8106 (mttt) REVERT: E 328 PHE cc_start: 0.9183 (t80) cc_final: 0.8688 (t80) REVERT: E 339 MET cc_start: 0.7604 (mtt) cc_final: 0.7378 (mtm) REVERT: E 388 LEU cc_start: 0.9258 (mt) cc_final: 0.8944 (mt) REVERT: F 136 TRP cc_start: 0.7969 (t-100) cc_final: 0.7449 (t-100) REVERT: F 194 GLN cc_start: 0.8927 (tp40) cc_final: 0.8693 (tp40) REVERT: F 195 LYS cc_start: 0.8879 (tppt) cc_final: 0.8563 (tppt) REVERT: F 196 LEU cc_start: 0.9015 (mt) cc_final: 0.8810 (mt) REVERT: F 289 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7215 (tpt170) REVERT: F 328 PHE cc_start: 0.8429 (t80) cc_final: 0.8086 (t80) REVERT: F 332 LEU cc_start: 0.9320 (mt) cc_final: 0.9060 (mt) REVERT: F 339 MET cc_start: 0.8506 (mtt) cc_final: 0.7335 (ttt) REVERT: F 396 HIS cc_start: 0.8760 (t-90) cc_final: 0.8446 (t70) REVERT: P 66 GLN cc_start: 0.8814 (tt0) cc_final: 0.8549 (tp-100) REVERT: P 67 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7964 (mm-30) REVERT: P 71 GLN cc_start: 0.9388 (mt0) cc_final: 0.8899 (mp10) REVERT: P 78 LYS cc_start: 0.9169 (mttt) cc_final: 0.8567 (mttt) REVERT: P 79 HIS cc_start: 0.8714 (t70) cc_final: 0.8265 (t70) REVERT: P 80 ILE cc_start: 0.9733 (mt) cc_final: 0.9526 (mm) REVERT: P 83 GLN cc_start: 0.9355 (mm-40) cc_final: 0.9110 (mm-40) REVERT: P 87 LEU cc_start: 0.9473 (mt) cc_final: 0.9189 (mt) REVERT: P 93 GLN cc_start: 0.8663 (mt0) cc_final: 0.7341 (mt0) REVERT: P 151 LEU cc_start: 0.9228 (mt) cc_final: 0.9004 (mt) REVERT: P 162 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8755 (mmmm) REVERT: P 167 LEU cc_start: 0.8704 (tp) cc_final: 0.8221 (tp) REVERT: P 171 LEU cc_start: 0.8588 (mt) cc_final: 0.8186 (tt) REVERT: P 204 GLN cc_start: 0.8716 (tp40) cc_final: 0.8369 (pm20) REVERT: P 212 VAL cc_start: 0.9491 (t) cc_final: 0.9105 (m) REVERT: P 218 HIS cc_start: 0.8526 (t-90) cc_final: 0.8188 (t-90) REVERT: P 223 GLU cc_start: 0.8206 (tp30) cc_final: 0.7296 (tp30) REVERT: P 226 PHE cc_start: 0.9531 (m-10) cc_final: 0.8922 (m-10) REVERT: P 243 VAL cc_start: 0.9299 (t) cc_final: 0.8711 (t) REVERT: P 259 ASP cc_start: 0.8592 (m-30) cc_final: 0.8355 (m-30) REVERT: P 260 TYR cc_start: 0.8580 (m-10) cc_final: 0.7941 (m-10) REVERT: P 264 GLN cc_start: 0.9398 (tt0) cc_final: 0.9065 (tm-30) REVERT: P 272 PHE cc_start: 0.8310 (p90) cc_final: 0.7914 (p90) REVERT: Z 5 LEU cc_start: 0.9156 (pp) cc_final: 0.8393 (pp) REVERT: Z 7 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7421 (ttp-170) REVERT: Z 26 PHE cc_start: 0.8737 (m-80) cc_final: 0.8502 (m-80) REVERT: Z 33 TYR cc_start: 0.9086 (t80) cc_final: 0.8465 (t80) REVERT: Z 84 LEU cc_start: 0.6774 (tp) cc_final: 0.6540 (tp) REVERT: Z 90 ASN cc_start: 0.8508 (t0) cc_final: 0.8016 (t0) REVERT: Z 92 GLU cc_start: 0.8143 (tp30) cc_final: 0.7617 (pm20) REVERT: Z 113 ASP cc_start: 0.7488 (m-30) cc_final: 0.7186 (m-30) REVERT: Z 125 GLN cc_start: 0.8998 (tt0) cc_final: 0.8396 (tm-30) REVERT: Z 127 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8422 (tt0) REVERT: Z 141 PHE cc_start: 0.8376 (p90) cc_final: 0.7694 (p90) REVERT: Z 191 HIS cc_start: 0.8422 (m90) cc_final: 0.7991 (m90) REVERT: Z 192 LYS cc_start: 0.8764 (tttm) cc_final: 0.8460 (tttt) REVERT: Z 194 ASN cc_start: 0.8891 (m-40) cc_final: 0.8643 (m110) outliers start: 0 outliers final: 0 residues processed: 896 average time/residue: 0.1570 time to fit residues: 209.9640 Evaluate side-chains 593 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN B 103 ASN B 208 GLN C 194 GLN C 374 ASN C 396 HIS D 47 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN E 286 GLN E 401 GLN P 79 HIS ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 264 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 GLN Z 125 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090098 restraints weight = 60611.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093078 restraints weight = 37600.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.095183 restraints weight = 26324.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096623 restraints weight = 20131.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.097638 restraints weight = 16574.977| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20823 Z= 0.166 Angle : 0.786 11.464 28246 Z= 0.404 Chirality : 0.050 0.277 3359 Planarity : 0.006 0.085 3526 Dihedral : 13.739 179.059 2944 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.68 % Favored : 90.16 % Rotamer: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.15), residues: 2541 helix: -1.44 (0.13), residues: 1131 sheet: -2.31 (0.25), residues: 345 loop : -2.83 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 386 TYR 0.031 0.002 TYR A 331 PHE 0.030 0.002 PHE E 393 TRP 0.027 0.003 TRP A 125 HIS 0.009 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (20809) covalent geometry : angle 0.78637 / 0.40 (28244) SS BOND : bond 0.00656 / 0.35 ( 1) SS BOND : angle 1.77107 / 1.18 ( 2) hydrogen bonds : bond 0.04930 / 3.34 ( 961) hydrogen bonds : angle 5.96887 / 4.14 ( 2766) Misc. bond : bond 0.00392 / 0.25 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 803 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8679 (m-30) cc_final: 0.8210 (p0) REVERT: A 173 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6220 (mpt-90) REVERT: A 188 LEU cc_start: 0.9612 (tp) cc_final: 0.9396 (tp) REVERT: A 200 LEU cc_start: 0.9208 (mt) cc_final: 0.8481 (tt) REVERT: A 233 PHE cc_start: 0.7348 (m-80) cc_final: 0.6763 (m-80) REVERT: A 285 ASP cc_start: 0.9095 (m-30) cc_final: 0.8796 (m-30) REVERT: A 286 GLN cc_start: 0.9144 (tt0) cc_final: 0.8907 (tt0) REVERT: A 290 HIS cc_start: 0.8094 (m90) cc_final: 0.7511 (m90) REVERT: A 331 TYR cc_start: 0.8280 (m-80) cc_final: 0.7720 (m-80) REVERT: A 336 GLU cc_start: 0.8674 (tp30) cc_final: 0.8464 (tp30) REVERT: A 358 MET cc_start: 0.8270 (mtm) cc_final: 0.8023 (tmm) REVERT: A 377 SER cc_start: 0.7070 (m) cc_final: 0.6245 (t) REVERT: A 391 LEU cc_start: 0.9266 (mt) cc_final: 0.9066 (mt) REVERT: A 393 PHE cc_start: 0.8831 (t80) cc_final: 0.8531 (t80) REVERT: A 408 GLU cc_start: 0.6236 (mp0) cc_final: 0.5976 (tp30) REVERT: A 419 ASP cc_start: 0.9182 (m-30) cc_final: 0.8978 (m-30) REVERT: B 68 ARG cc_start: 0.9042 (tpt90) cc_final: 0.8836 (tpt90) REVERT: B 127 LEU cc_start: 0.8832 (tp) cc_final: 0.8502 (tp) REVERT: B 141 TYR cc_start: 0.7442 (m-80) cc_final: 0.7185 (m-10) REVERT: B 188 LEU cc_start: 0.9654 (tp) cc_final: 0.9244 (tp) REVERT: B 189 CYS cc_start: 0.9136 (m) cc_final: 0.8438 (m) REVERT: B 211 GLU cc_start: 0.8580 (tt0) cc_final: 0.7915 (tp30) REVERT: B 218 PHE cc_start: 0.8717 (m-80) cc_final: 0.8119 (m-80) REVERT: B 231 LYS cc_start: 0.8407 (mttt) cc_final: 0.8014 (tmtt) REVERT: B 248 PHE cc_start: 0.9130 (m-80) cc_final: 0.8775 (m-10) REVERT: B 250 LEU cc_start: 0.9036 (tp) cc_final: 0.8819 (tp) REVERT: B 272 ASP cc_start: 0.7619 (m-30) cc_final: 0.7296 (m-30) REVERT: B 296 LEU cc_start: 0.9155 (mt) cc_final: 0.8582 (mt) REVERT: B 327 ILE cc_start: 0.9465 (mt) cc_final: 0.9149 (mt) REVERT: B 328 PHE cc_start: 0.8936 (t80) cc_final: 0.8014 (t80) REVERT: B 329 LYS cc_start: 0.9106 (mttt) cc_final: 0.8559 (mtmm) REVERT: B 335 LEU cc_start: 0.9743 (mt) cc_final: 0.9500 (mt) REVERT: C 23 VAL cc_start: 0.9012 (t) cc_final: 0.8435 (t) REVERT: C 34 LYS cc_start: 0.9000 (mttt) cc_final: 0.8583 (mmmm) REVERT: C 56 TYR cc_start: 0.6815 (t80) cc_final: 0.6395 (m-80) REVERT: C 58 TRP cc_start: 0.8847 (m-90) cc_final: 0.8415 (m-90) REVERT: C 98 HIS cc_start: 0.7181 (m-70) cc_final: 0.6781 (m90) REVERT: C 173 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7369 (mpt-90) REVERT: C 197 THR cc_start: 0.8814 (m) cc_final: 0.8595 (m) REVERT: C 198 ILE cc_start: 0.9361 (mm) cc_final: 0.9100 (mt) REVERT: C 212 ILE cc_start: 0.8486 (mm) cc_final: 0.8228 (mm) REVERT: C 228 LEU cc_start: 0.9541 (pp) cc_final: 0.8240 (pp) REVERT: C 231 LYS cc_start: 0.9225 (mttt) cc_final: 0.8993 (tmtt) REVERT: C 282 THR cc_start: 0.9540 (p) cc_final: 0.9307 (p) REVERT: C 283 GLN cc_start: 0.9027 (mm110) cc_final: 0.8341 (mm110) REVERT: C 339 MET cc_start: 0.6589 (ttp) cc_final: 0.6222 (tmm) REVERT: C 368 LYS cc_start: 0.9306 (pttm) cc_final: 0.9010 (pttp) REVERT: C 388 LEU cc_start: 0.9286 (mm) cc_final: 0.8975 (mm) REVERT: C 391 LEU cc_start: 0.9658 (mt) cc_final: 0.9076 (mt) REVERT: D 123 ASN cc_start: 0.8706 (m-40) cc_final: 0.7896 (m-40) REVERT: D 133 HIS cc_start: 0.7916 (t70) cc_final: 0.7688 (t70) REVERT: D 158 LEU cc_start: 0.8925 (tp) cc_final: 0.8340 (tt) REVERT: D 159 PHE cc_start: 0.6918 (m-80) cc_final: 0.6097 (m-80) REVERT: D 171 TRP cc_start: 0.7906 (p-90) cc_final: 0.7235 (p-90) REVERT: D 190 LYS cc_start: 0.9429 (mttt) cc_final: 0.9190 (mtmt) REVERT: D 192 LEU cc_start: 0.9648 (tp) cc_final: 0.9308 (tp) REVERT: D 209 LEU cc_start: 0.9212 (tp) cc_final: 0.8771 (tp) REVERT: D 248 PHE cc_start: 0.9313 (m-80) cc_final: 0.8952 (m-10) REVERT: D 252 ASP cc_start: 0.7993 (t0) cc_final: 0.7681 (t70) REVERT: D 255 GLU cc_start: 0.9040 (pt0) cc_final: 0.7730 (tt0) REVERT: D 281 LEU cc_start: 0.9131 (mt) cc_final: 0.8855 (mt) REVERT: D 296 LEU cc_start: 0.8602 (mt) cc_final: 0.7821 (mt) REVERT: D 303 GLU cc_start: 0.8129 (tp30) cc_final: 0.7756 (tp30) REVERT: D 328 PHE cc_start: 0.9045 (t80) cc_final: 0.8789 (t80) REVERT: D 329 LYS cc_start: 0.8851 (mttt) cc_final: 0.8575 (mmtt) REVERT: D 330 ILE cc_start: 0.9256 (tt) cc_final: 0.9030 (tt) REVERT: D 368 LYS cc_start: 0.9536 (tttt) cc_final: 0.9324 (tttm) REVERT: D 378 ARG cc_start: 0.8673 (mtt-85) cc_final: 0.7943 (mtt-85) REVERT: D 391 LEU cc_start: 0.9642 (mt) cc_final: 0.9385 (mt) REVERT: D 423 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8581 (mm-30) REVERT: D 424 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8118 (mt-10) REVERT: E 28 ARG cc_start: 0.7684 (mmt180) cc_final: 0.7319 (ttm110) REVERT: E 58 TRP cc_start: 0.6969 (m-90) cc_final: 0.5967 (m-90) REVERT: E 62 ASP cc_start: 0.8212 (m-30) cc_final: 0.7889 (t0) REVERT: E 72 SER cc_start: 0.7821 (p) cc_final: 0.7405 (m) REVERT: E 167 ASN cc_start: 0.9332 (m-40) cc_final: 0.8464 (p0) REVERT: E 189 CYS cc_start: 0.9044 (t) cc_final: 0.8777 (t) REVERT: E 236 ILE cc_start: 0.9571 (mt) cc_final: 0.9095 (mt) REVERT: E 290 HIS cc_start: 0.9158 (m90) cc_final: 0.8953 (m90) REVERT: E 328 PHE cc_start: 0.8957 (t80) cc_final: 0.8314 (t80) REVERT: E 388 LEU cc_start: 0.9472 (mt) cc_final: 0.9199 (mt) REVERT: E 390 LYS cc_start: 0.9241 (tptm) cc_final: 0.8825 (tptt) REVERT: F 171 TRP cc_start: 0.8638 (p-90) cc_final: 0.8347 (p-90) REVERT: F 250 LEU cc_start: 0.8865 (tp) cc_final: 0.8580 (pp) REVERT: F 328 PHE cc_start: 0.8449 (t80) cc_final: 0.8088 (t80) REVERT: F 332 LEU cc_start: 0.9442 (mt) cc_final: 0.8865 (mt) REVERT: F 334 CYS cc_start: 0.9084 (m) cc_final: 0.8607 (m) REVERT: F 339 MET cc_start: 0.8386 (mtt) cc_final: 0.7262 (ttp) REVERT: F 396 HIS cc_start: 0.8910 (t-90) cc_final: 0.8607 (t70) REVERT: P 67 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8066 (mm-30) REVERT: P 71 GLN cc_start: 0.9265 (mt0) cc_final: 0.8979 (mp10) REVERT: P 76 LEU cc_start: 0.9393 (tp) cc_final: 0.9127 (tp) REVERT: P 78 LYS cc_start: 0.8800 (mttt) cc_final: 0.8516 (mttp) REVERT: P 79 HIS cc_start: 0.8280 (t-90) cc_final: 0.7842 (t70) REVERT: P 93 GLN cc_start: 0.8057 (mt0) cc_final: 0.7100 (mt0) REVERT: P 125 GLN cc_start: 0.7037 (mm-40) cc_final: 0.5781 (pm20) REVERT: P 139 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8734 (mm-30) REVERT: P 151 LEU cc_start: 0.8826 (mt) cc_final: 0.8598 (mt) REVERT: P 212 VAL cc_start: 0.9389 (t) cc_final: 0.9076 (m) REVERT: P 214 MET cc_start: 0.7589 (mtp) cc_final: 0.7221 (mtp) REVERT: P 218 HIS cc_start: 0.8645 (t-90) cc_final: 0.8259 (t-90) REVERT: P 229 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8083 (mmtm) REVERT: P 243 VAL cc_start: 0.9159 (t) cc_final: 0.8516 (t) REVERT: P 257 TRP cc_start: 0.8376 (m100) cc_final: 0.8017 (m100) REVERT: P 264 GLN cc_start: 0.9323 (tt0) cc_final: 0.9048 (tm-30) REVERT: P 269 PHE cc_start: 0.8729 (t80) cc_final: 0.8095 (t80) REVERT: Q 130 ILE cc_start: 0.9112 (mt) cc_final: 0.8812 (mt) REVERT: Z 24 PHE cc_start: 0.7964 (m-80) cc_final: 0.7395 (m-80) REVERT: Z 33 TYR cc_start: 0.8859 (t80) cc_final: 0.8411 (t80) REVERT: Z 47 GLN cc_start: 0.7624 (tp40) cc_final: 0.7390 (tp-100) REVERT: Z 75 TRP cc_start: 0.8520 (m-10) cc_final: 0.8112 (m-10) REVERT: Z 92 GLU cc_start: 0.7936 (tp30) cc_final: 0.7736 (pm20) REVERT: Z 194 ASN cc_start: 0.9085 (m-40) cc_final: 0.8840 (m110) outliers start: 1 outliers final: 0 residues processed: 803 average time/residue: 0.1450 time to fit residues: 179.5613 Evaluate side-chains 606 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 221 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS A 178 HIS A 194 GLN C 178 HIS C 283 GLN C 396 HIS ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS E 27 GLN ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN F 208 GLN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 264 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN Z 101 GLN ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085319 restraints weight = 63074.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088133 restraints weight = 38898.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090049 restraints weight = 27243.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091387 restraints weight = 20993.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092306 restraints weight = 17340.513| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20823 Z= 0.264 Angle : 0.841 14.259 28246 Z= 0.426 Chirality : 0.050 0.273 3359 Planarity : 0.006 0.097 3526 Dihedral : 13.005 179.032 2944 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.06 % Favored : 88.67 % Rotamer: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.15), residues: 2541 helix: -1.04 (0.14), residues: 1149 sheet: -2.08 (0.26), residues: 328 loop : -2.73 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 386 TYR 0.031 0.002 TYR F 204 PHE 0.047 0.002 PHE P 72 TRP 0.031 0.002 TRP A 125 HIS 0.011 0.002 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.26 (20809) covalent geometry : angle 0.84137 / 0.43 (28244) SS BOND : bond 0.00496 / 0.26 ( 1) SS BOND : angle 1.00288 / 0.67 ( 2) hydrogen bonds : bond 0.04902 / 3.30 ( 961) hydrogen bonds : angle 6.01811 / 4.18 ( 2766) Misc. bond : bond 0.00470 / 0.32 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 677 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8747 (m-30) cc_final: 0.8455 (p0) REVERT: A 146 LYS cc_start: 0.9317 (ptpp) cc_final: 0.9088 (ptpp) REVERT: A 150 LEU cc_start: 0.9407 (tp) cc_final: 0.9188 (tp) REVERT: A 151 ASP cc_start: 0.8484 (m-30) cc_final: 0.8191 (m-30) REVERT: A 173 ARG cc_start: 0.7441 (mtt90) cc_final: 0.6621 (mpt-90) REVERT: A 282 THR cc_start: 0.9272 (p) cc_final: 0.8814 (t) REVERT: A 286 GLN cc_start: 0.9110 (tt0) cc_final: 0.8547 (pt0) REVERT: A 290 HIS cc_start: 0.8226 (m90) cc_final: 0.7729 (m90) REVERT: A 328 PHE cc_start: 0.8903 (t80) cc_final: 0.8657 (t80) REVERT: A 331 TYR cc_start: 0.8485 (m-80) cc_final: 0.7821 (m-80) REVERT: A 358 MET cc_start: 0.8518 (mtm) cc_final: 0.8166 (tmm) REVERT: A 377 SER cc_start: 0.7262 (m) cc_final: 0.6771 (t) REVERT: A 390 LYS cc_start: 0.8759 (tptp) cc_final: 0.8385 (tptp) REVERT: A 391 LEU cc_start: 0.9376 (mt) cc_final: 0.9140 (mt) REVERT: A 393 PHE cc_start: 0.8997 (t80) cc_final: 0.8513 (t80) REVERT: B 68 ARG cc_start: 0.8999 (tpt90) cc_final: 0.8757 (tpt90) REVERT: B 154 MET cc_start: 0.9296 (mmm) cc_final: 0.9061 (mmm) REVERT: B 188 LEU cc_start: 0.9521 (tp) cc_final: 0.9185 (tp) REVERT: B 189 CYS cc_start: 0.9158 (m) cc_final: 0.8451 (m) REVERT: B 231 LYS cc_start: 0.8509 (mttt) cc_final: 0.8263 (tmtt) REVERT: B 248 PHE cc_start: 0.9223 (m-80) cc_final: 0.8865 (m-80) REVERT: B 296 LEU cc_start: 0.9200 (mt) cc_final: 0.8658 (mt) REVERT: B 327 ILE cc_start: 0.9640 (mt) cc_final: 0.9323 (mt) REVERT: B 328 PHE cc_start: 0.9068 (t80) cc_final: 0.8245 (t80) REVERT: B 329 LYS cc_start: 0.9095 (mttt) cc_final: 0.8627 (mtmm) REVERT: B 399 TYR cc_start: 0.8838 (m-80) cc_final: 0.8429 (m-80) REVERT: C 56 TYR cc_start: 0.6824 (t80) cc_final: 0.6486 (m-80) REVERT: C 98 HIS cc_start: 0.6968 (m-70) cc_final: 0.6742 (m-70) REVERT: C 124 HIS cc_start: 0.8138 (t-170) cc_final: 0.7894 (t-170) REVERT: C 212 ILE cc_start: 0.8630 (mm) cc_final: 0.8029 (mm) REVERT: C 224 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6602 (tm-30) REVERT: C 253 GLN cc_start: 0.8858 (mt0) cc_final: 0.8199 (mp10) REVERT: C 368 LYS cc_start: 0.9301 (pttm) cc_final: 0.8819 (pttp) REVERT: C 391 LEU cc_start: 0.9696 (mt) cc_final: 0.9113 (mt) REVERT: C 407 ILE cc_start: 0.9034 (pt) cc_final: 0.7720 (pt) REVERT: D 48 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7981 (mtt180) REVERT: D 123 ASN cc_start: 0.8776 (m-40) cc_final: 0.7860 (m-40) REVERT: D 132 PHE cc_start: 0.9026 (m-10) cc_final: 0.8765 (m-80) REVERT: D 136 TRP cc_start: 0.8720 (t-100) cc_final: 0.8492 (t60) REVERT: D 141 TYR cc_start: 0.8661 (m-80) cc_final: 0.8437 (m-80) REVERT: D 158 LEU cc_start: 0.9092 (tp) cc_final: 0.8610 (tt) REVERT: D 171 TRP cc_start: 0.8228 (p-90) cc_final: 0.6870 (p-90) REVERT: D 189 CYS cc_start: 0.8835 (m) cc_final: 0.8582 (m) REVERT: D 190 LYS cc_start: 0.9491 (mttt) cc_final: 0.9224 (mtmt) REVERT: D 192 LEU cc_start: 0.9635 (tp) cc_final: 0.9307 (tp) REVERT: D 209 LEU cc_start: 0.8642 (tp) cc_final: 0.8009 (tp) REVERT: D 248 PHE cc_start: 0.9359 (m-80) cc_final: 0.8996 (m-80) REVERT: D 278 ASN cc_start: 0.8897 (p0) cc_final: 0.8493 (p0) REVERT: D 281 LEU cc_start: 0.9280 (mt) cc_final: 0.8937 (mt) REVERT: D 303 GLU cc_start: 0.8167 (tp30) cc_final: 0.7963 (tp30) REVERT: D 328 PHE cc_start: 0.9161 (t80) cc_final: 0.8868 (t80) REVERT: D 329 LYS cc_start: 0.8895 (mttt) cc_final: 0.8563 (mmtt) REVERT: D 330 ILE cc_start: 0.9267 (tt) cc_final: 0.9056 (tt) REVERT: D 391 LEU cc_start: 0.9580 (mt) cc_final: 0.9279 (mt) REVERT: D 423 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8755 (tp30) REVERT: D 424 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7857 (mt-10) REVERT: E 58 TRP cc_start: 0.7072 (m-90) cc_final: 0.6070 (m-90) REVERT: E 62 ASP cc_start: 0.8250 (m-30) cc_final: 0.7888 (t0) REVERT: E 211 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6974 (tm-30) REVERT: E 255 GLU cc_start: 0.8500 (pm20) cc_final: 0.8217 (pp20) REVERT: E 304 LYS cc_start: 0.9249 (pptt) cc_final: 0.9047 (pptt) REVERT: E 316 LYS cc_start: 0.8055 (mttt) cc_final: 0.7749 (mttt) REVERT: E 328 PHE cc_start: 0.9042 (t80) cc_final: 0.8398 (t80) REVERT: E 335 LEU cc_start: 0.9066 (mt) cc_final: 0.8632 (mt) REVERT: E 339 MET cc_start: 0.7107 (mtm) cc_final: 0.6710 (mpp) REVERT: E 388 LEU cc_start: 0.9379 (mt) cc_final: 0.9081 (mt) REVERT: F 159 PHE cc_start: 0.8653 (m-80) cc_final: 0.8416 (m-80) REVERT: F 171 TRP cc_start: 0.8555 (p-90) cc_final: 0.8242 (p-90) REVERT: F 194 GLN cc_start: 0.8412 (tp40) cc_final: 0.8132 (tp40) REVERT: F 195 LYS cc_start: 0.8819 (tppt) cc_final: 0.8610 (tppt) REVERT: F 196 LEU cc_start: 0.8717 (mt) cc_final: 0.8499 (mt) REVERT: F 250 LEU cc_start: 0.9084 (tp) cc_final: 0.8723 (pp) REVERT: F 328 PHE cc_start: 0.8704 (t80) cc_final: 0.8471 (t80) REVERT: F 332 LEU cc_start: 0.9247 (mt) cc_final: 0.8935 (mt) REVERT: F 339 MET cc_start: 0.8411 (mtt) cc_final: 0.8019 (mpp) REVERT: F 396 HIS cc_start: 0.9107 (t-90) cc_final: 0.8660 (t70) REVERT: F 401 GLN cc_start: 0.8439 (mt0) cc_final: 0.8133 (mm110) REVERT: F 414 LEU cc_start: 0.9450 (mt) cc_final: 0.9192 (mt) REVERT: P 55 MET cc_start: 0.7666 (tpt) cc_final: 0.5778 (mpp) REVERT: P 60 PHE cc_start: 0.8352 (m-10) cc_final: 0.7909 (m-10) REVERT: P 67 GLU cc_start: 0.8609 (mt-10) cc_final: 0.7971 (mm-30) REVERT: P 71 GLN cc_start: 0.9315 (mt0) cc_final: 0.8976 (mp10) REVERT: P 78 LYS cc_start: 0.8932 (mttt) cc_final: 0.8441 (mttt) REVERT: P 139 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8419 (tm-30) REVERT: P 141 PHE cc_start: 0.9078 (t80) cc_final: 0.8822 (t80) REVERT: P 150 VAL cc_start: 0.9357 (t) cc_final: 0.9142 (t) REVERT: P 151 LEU cc_start: 0.9009 (mt) cc_final: 0.8700 (mt) REVERT: P 186 CYS cc_start: 0.9502 (m) cc_final: 0.8248 (m) REVERT: P 202 GLU cc_start: 0.9253 (pm20) cc_final: 0.9044 (pm20) REVERT: P 212 VAL cc_start: 0.9435 (t) cc_final: 0.9144 (m) REVERT: P 218 HIS cc_start: 0.8725 (t-90) cc_final: 0.8415 (t-90) REVERT: P 242 THR cc_start: 0.8322 (m) cc_final: 0.8052 (m) REVERT: P 272 PHE cc_start: 0.8551 (p90) cc_final: 0.8165 (p90) REVERT: P 274 GLU cc_start: 0.6146 (mp0) cc_final: 0.5918 (mp0) REVERT: Q 130 ILE cc_start: 0.9127 (mt) cc_final: 0.8804 (mt) REVERT: Z 4 GLN cc_start: 0.6832 (mt0) cc_final: 0.6622 (mt0) REVERT: Z 20 VAL cc_start: 0.9742 (p) cc_final: 0.9510 (p) REVERT: Z 24 PHE cc_start: 0.8174 (m-80) cc_final: 0.7341 (m-80) REVERT: Z 33 TYR cc_start: 0.8843 (t80) cc_final: 0.8356 (t80) REVERT: Z 75 TRP cc_start: 0.8657 (m-10) cc_final: 0.8417 (m-10) REVERT: Z 117 ARG cc_start: 0.7064 (mtp180) cc_final: 0.6841 (mtp85) REVERT: Z 156 TYR cc_start: 0.8222 (t80) cc_final: 0.8008 (t80) REVERT: Z 174 PHE cc_start: 0.7758 (m-80) cc_final: 0.7124 (t80) REVERT: Z 194 ASN cc_start: 0.8981 (m-40) cc_final: 0.8634 (p0) outliers start: 1 outliers final: 1 residues processed: 677 average time/residue: 0.1405 time to fit residues: 148.0678 Evaluate side-chains 524 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 194 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 219 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 152 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 ASN ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.112403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086194 restraints weight = 62761.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089026 restraints weight = 38881.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091008 restraints weight = 27470.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092415 restraints weight = 21256.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093429 restraints weight = 17638.587| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20823 Z= 0.214 Angle : 0.781 10.670 28246 Z= 0.396 Chirality : 0.049 0.273 3359 Planarity : 0.005 0.091 3526 Dihedral : 12.422 179.266 2944 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.35 % Favored : 89.37 % Rotamer: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.16), residues: 2541 helix: -0.75 (0.14), residues: 1157 sheet: -1.80 (0.26), residues: 321 loop : -2.57 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 173 TYR 0.034 0.002 TYR F 204 PHE 0.032 0.002 PHE P 72 TRP 0.040 0.003 TRP P 257 HIS 0.009 0.002 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (20809) covalent geometry : angle 0.78060 / 0.40 (28244) SS BOND : bond 0.00358 / 0.19 ( 1) SS BOND : angle 0.54173 / 0.36 ( 2) hydrogen bonds : bond 0.04510 / 3.05 ( 961) hydrogen bonds : angle 5.79209 / 4.02 ( 2766) Misc. bond : bond 0.00266 / 0.20 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 640 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8766 (m-30) cc_final: 0.8465 (p0) REVERT: A 146 LYS cc_start: 0.9280 (ptpp) cc_final: 0.8943 (ptpp) REVERT: A 154 MET cc_start: 0.9208 (ttm) cc_final: 0.8951 (ttp) REVERT: A 173 ARG cc_start: 0.7492 (mtt90) cc_final: 0.6693 (mpt-90) REVERT: A 247 VAL cc_start: 0.9156 (t) cc_final: 0.8928 (t) REVERT: A 287 ILE cc_start: 0.8545 (pt) cc_final: 0.8220 (pt) REVERT: A 290 HIS cc_start: 0.8152 (m90) cc_final: 0.7601 (m90) REVERT: A 295 ILE cc_start: 0.9122 (mm) cc_final: 0.8885 (mm) REVERT: A 296 LEU cc_start: 0.9581 (mt) cc_final: 0.9379 (mt) REVERT: A 331 TYR cc_start: 0.8595 (m-10) cc_final: 0.8197 (m-80) REVERT: A 358 MET cc_start: 0.8363 (mtm) cc_final: 0.8154 (tmm) REVERT: A 377 SER cc_start: 0.7269 (m) cc_final: 0.6885 (p) REVERT: A 381 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 390 LYS cc_start: 0.8728 (tptp) cc_final: 0.8326 (tptp) REVERT: A 391 LEU cc_start: 0.9334 (mt) cc_final: 0.9052 (mt) REVERT: A 393 PHE cc_start: 0.8952 (t80) cc_final: 0.8558 (t80) REVERT: A 399 TYR cc_start: 0.8175 (m-80) cc_final: 0.7967 (m-80) REVERT: B 68 ARG cc_start: 0.8947 (tpt90) cc_final: 0.8669 (tpt90) REVERT: B 141 TYR cc_start: 0.7035 (m-10) cc_final: 0.6351 (m-10) REVERT: B 188 LEU cc_start: 0.9436 (tp) cc_final: 0.9226 (tp) REVERT: B 189 CYS cc_start: 0.9134 (m) cc_final: 0.8538 (m) REVERT: B 231 LYS cc_start: 0.8452 (mttt) cc_final: 0.8182 (tmtt) REVERT: B 248 PHE cc_start: 0.9221 (m-80) cc_final: 0.8898 (m-80) REVERT: B 296 LEU cc_start: 0.9235 (mt) cc_final: 0.8670 (mt) REVERT: B 327 ILE cc_start: 0.9628 (mt) cc_final: 0.9254 (mt) REVERT: B 328 PHE cc_start: 0.9047 (t80) cc_final: 0.8139 (t80) REVERT: B 329 LYS cc_start: 0.9082 (mttt) cc_final: 0.8552 (mtmm) REVERT: B 399 TYR cc_start: 0.8888 (m-80) cc_final: 0.8678 (m-80) REVERT: C 23 VAL cc_start: 0.9055 (t) cc_final: 0.8501 (t) REVERT: C 56 TYR cc_start: 0.6810 (t80) cc_final: 0.6480 (m-80) REVERT: C 98 HIS cc_start: 0.6874 (m-70) cc_final: 0.6529 (m90) REVERT: C 124 HIS cc_start: 0.8066 (t-170) cc_final: 0.7854 (t-170) REVERT: C 189 CYS cc_start: 0.8950 (m) cc_final: 0.8642 (m) REVERT: C 212 ILE cc_start: 0.8558 (mm) cc_final: 0.7935 (mm) REVERT: C 224 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6658 (tm-30) REVERT: C 228 LEU cc_start: 0.9439 (pp) cc_final: 0.8871 (pp) REVERT: C 248 PHE cc_start: 0.8971 (m-80) cc_final: 0.8748 (m-80) REVERT: C 368 LYS cc_start: 0.9220 (pttm) cc_final: 0.8840 (pttp) REVERT: C 388 LEU cc_start: 0.9426 (mm) cc_final: 0.9194 (mm) REVERT: C 391 LEU cc_start: 0.9649 (mt) cc_final: 0.8991 (mt) REVERT: D 123 ASN cc_start: 0.8789 (m-40) cc_final: 0.7953 (m-40) REVERT: D 136 TRP cc_start: 0.8696 (t-100) cc_final: 0.7874 (t60) REVERT: D 141 TYR cc_start: 0.8882 (m-80) cc_final: 0.8623 (m-80) REVERT: D 158 LEU cc_start: 0.9048 (tp) cc_final: 0.8564 (tt) REVERT: D 171 TRP cc_start: 0.7639 (p-90) cc_final: 0.7056 (p-90) REVERT: D 188 LEU cc_start: 0.9063 (tt) cc_final: 0.8861 (tt) REVERT: D 189 CYS cc_start: 0.8889 (m) cc_final: 0.8537 (m) REVERT: D 192 LEU cc_start: 0.9674 (tp) cc_final: 0.9238 (tp) REVERT: D 195 LYS cc_start: 0.9441 (tppt) cc_final: 0.8569 (tppt) REVERT: D 196 LEU cc_start: 0.9642 (mt) cc_final: 0.9438 (mt) REVERT: D 248 PHE cc_start: 0.9255 (m-80) cc_final: 0.8796 (m-10) REVERT: D 281 LEU cc_start: 0.9249 (mt) cc_final: 0.8994 (mt) REVERT: D 316 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8289 (mtpt) REVERT: D 328 PHE cc_start: 0.9152 (t80) cc_final: 0.8764 (t80) REVERT: D 329 LYS cc_start: 0.8942 (mttt) cc_final: 0.8581 (mmtt) REVERT: D 330 ILE cc_start: 0.9263 (tt) cc_final: 0.9030 (tt) REVERT: D 391 LEU cc_start: 0.9598 (mt) cc_final: 0.9312 (mt) REVERT: D 424 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8042 (mt-10) REVERT: E 24 GLU cc_start: 0.7703 (pp20) cc_final: 0.7445 (pp20) REVERT: E 26 HIS cc_start: 0.6369 (t-90) cc_final: 0.6167 (t70) REVERT: E 72 SER cc_start: 0.8010 (p) cc_final: 0.7233 (m) REVERT: E 189 CYS cc_start: 0.9223 (t) cc_final: 0.8964 (t) REVERT: E 255 GLU cc_start: 0.8476 (pm20) cc_final: 0.8157 (pp20) REVERT: E 316 LYS cc_start: 0.8164 (mttt) cc_final: 0.7912 (mttt) REVERT: E 328 PHE cc_start: 0.9039 (t80) cc_final: 0.8434 (t80) REVERT: E 335 LEU cc_start: 0.9055 (mt) cc_final: 0.8617 (mt) REVERT: E 339 MET cc_start: 0.6932 (mtm) cc_final: 0.6496 (mpp) REVERT: E 388 LEU cc_start: 0.9402 (mt) cc_final: 0.9087 (mt) REVERT: F 196 LEU cc_start: 0.8668 (mt) cc_final: 0.8431 (mt) REVERT: F 250 LEU cc_start: 0.8991 (tp) cc_final: 0.8737 (pp) REVERT: F 328 PHE cc_start: 0.8636 (t80) cc_final: 0.8218 (t80) REVERT: F 332 LEU cc_start: 0.9250 (mt) cc_final: 0.8841 (mt) REVERT: F 339 MET cc_start: 0.8435 (mtt) cc_final: 0.8046 (mpp) REVERT: F 358 MET cc_start: 0.8591 (tpp) cc_final: 0.7807 (ppp) REVERT: F 396 HIS cc_start: 0.9052 (t-90) cc_final: 0.8733 (t70) REVERT: F 414 LEU cc_start: 0.9499 (mt) cc_final: 0.9273 (mt) REVERT: P 67 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7989 (mm-30) REVERT: P 71 GLN cc_start: 0.9230 (mt0) cc_final: 0.9015 (mp10) REVERT: P 78 LYS cc_start: 0.8897 (mttt) cc_final: 0.8437 (mttt) REVERT: P 131 LEU cc_start: 0.9555 (tp) cc_final: 0.9170 (tt) REVERT: P 135 LEU cc_start: 0.9347 (mt) cc_final: 0.9078 (mt) REVERT: P 157 ASN cc_start: 0.8322 (p0) cc_final: 0.8089 (p0) REVERT: P 186 CYS cc_start: 0.9467 (m) cc_final: 0.8944 (p) REVERT: P 202 GLU cc_start: 0.9111 (pm20) cc_final: 0.8909 (pm20) REVERT: P 212 VAL cc_start: 0.9461 (t) cc_final: 0.9166 (m) REVERT: P 218 HIS cc_start: 0.8806 (t-90) cc_final: 0.8467 (t-90) REVERT: P 242 THR cc_start: 0.8190 (m) cc_final: 0.7424 (m) REVERT: P 257 TRP cc_start: 0.8333 (m100) cc_final: 0.8088 (m100) REVERT: Q 130 ILE cc_start: 0.9231 (mt) cc_final: 0.8620 (mt) REVERT: Q 131 LEU cc_start: 0.9052 (mt) cc_final: 0.8797 (tp) REVERT: Z 4 GLN cc_start: 0.7273 (mt0) cc_final: 0.7008 (mt0) REVERT: Z 9 GLN cc_start: 0.7685 (mp10) cc_final: 0.6982 (mp10) REVERT: Z 20 VAL cc_start: 0.9713 (p) cc_final: 0.9441 (p) REVERT: Z 24 PHE cc_start: 0.8215 (m-80) cc_final: 0.7436 (m-80) REVERT: Z 26 PHE cc_start: 0.8687 (m-80) cc_final: 0.8325 (m-80) REVERT: Z 29 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7966 (t0) REVERT: Z 47 GLN cc_start: 0.8053 (tp40) cc_final: 0.7718 (tp40) REVERT: Z 49 TYR cc_start: 0.6512 (m-80) cc_final: 0.5121 (m-80) REVERT: Z 75 TRP cc_start: 0.8845 (m-10) cc_final: 0.8460 (m-10) REVERT: Z 117 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6751 (mtp85) REVERT: Z 156 TYR cc_start: 0.8205 (t80) cc_final: 0.8000 (t80) REVERT: Z 192 LYS cc_start: 0.8694 (tttm) cc_final: 0.8296 (tptm) REVERT: Z 194 ASN cc_start: 0.8976 (m-40) cc_final: 0.8457 (p0) outliers start: 2 outliers final: 1 residues processed: 642 average time/residue: 0.1383 time to fit residues: 140.1485 Evaluate side-chains 508 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 506 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 182 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 GLN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086956 restraints weight = 61381.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089843 restraints weight = 37713.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091904 restraints weight = 26527.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093324 restraints weight = 20318.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.094334 restraints weight = 16824.203| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20823 Z= 0.184 Angle : 0.750 10.335 28246 Z= 0.383 Chirality : 0.049 0.273 3359 Planarity : 0.005 0.090 3526 Dihedral : 12.003 176.303 2944 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.64 % Favored : 90.08 % Rotamer: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.16), residues: 2541 helix: -0.46 (0.15), residues: 1150 sheet: -1.76 (0.27), residues: 314 loop : -2.37 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 289 TYR 0.038 0.002 TYR F 204 PHE 0.032 0.002 PHE P 72 TRP 0.039 0.002 TRP A 221 HIS 0.008 0.001 HIS E 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (20809) covalent geometry : angle 0.74969 / 0.38 (28244) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 0.49160 / 0.33 ( 2) hydrogen bonds : bond 0.04292 / 2.88 ( 961) hydrogen bonds : angle 5.64087 / 3.92 ( 2766) Misc. bond : bond 0.00360 / 0.25 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 640 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8764 (m-30) cc_final: 0.8221 (p0) REVERT: A 146 LYS cc_start: 0.9343 (ptpp) cc_final: 0.8992 (ptpp) REVERT: A 151 ASP cc_start: 0.8088 (m-30) cc_final: 0.7734 (m-30) REVERT: A 154 MET cc_start: 0.9172 (ttm) cc_final: 0.8901 (ttm) REVERT: A 173 ARG cc_start: 0.7791 (mtt90) cc_final: 0.6739 (mpt-90) REVERT: A 233 PHE cc_start: 0.7540 (m-80) cc_final: 0.6969 (m-80) REVERT: A 252 ASP cc_start: 0.9026 (p0) cc_final: 0.8791 (p0) REVERT: A 287 ILE cc_start: 0.8526 (pt) cc_final: 0.8203 (pt) REVERT: A 290 HIS cc_start: 0.8169 (m90) cc_final: 0.7660 (m90) REVERT: A 295 ILE cc_start: 0.9130 (mm) cc_final: 0.8885 (mm) REVERT: A 328 PHE cc_start: 0.8872 (t80) cc_final: 0.8637 (t80) REVERT: A 331 TYR cc_start: 0.8591 (m-10) cc_final: 0.8337 (m-80) REVERT: A 356 LEU cc_start: 0.9528 (mt) cc_final: 0.9117 (tp) REVERT: A 358 MET cc_start: 0.8338 (mtm) cc_final: 0.8130 (tmm) REVERT: A 377 SER cc_start: 0.7268 (m) cc_final: 0.6849 (t) REVERT: A 391 LEU cc_start: 0.9305 (mt) cc_final: 0.9017 (mt) REVERT: A 399 TYR cc_start: 0.8157 (m-80) cc_final: 0.7933 (m-80) REVERT: B 68 ARG cc_start: 0.9015 (tpt90) cc_final: 0.8658 (tpt90) REVERT: B 141 TYR cc_start: 0.6947 (m-10) cc_final: 0.6597 (m-10) REVERT: B 189 CYS cc_start: 0.9183 (m) cc_final: 0.8706 (m) REVERT: B 231 LYS cc_start: 0.8443 (mttt) cc_final: 0.8210 (tmtt) REVERT: B 248 PHE cc_start: 0.9125 (m-80) cc_final: 0.8771 (m-80) REVERT: B 296 LEU cc_start: 0.9178 (mt) cc_final: 0.8547 (mt) REVERT: B 327 ILE cc_start: 0.9593 (mt) cc_final: 0.9175 (mt) REVERT: B 328 PHE cc_start: 0.9080 (t80) cc_final: 0.8318 (t80) REVERT: B 329 LYS cc_start: 0.9059 (mttt) cc_final: 0.8748 (mmmm) REVERT: B 424 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7994 (mt-10) REVERT: C 23 VAL cc_start: 0.9057 (t) cc_final: 0.8548 (t) REVERT: C 56 TYR cc_start: 0.6954 (t80) cc_final: 0.6727 (m-80) REVERT: C 98 HIS cc_start: 0.6849 (m-70) cc_final: 0.6478 (m90) REVERT: C 189 CYS cc_start: 0.8870 (m) cc_final: 0.8643 (m) REVERT: C 212 ILE cc_start: 0.8496 (mm) cc_final: 0.7966 (mm) REVERT: C 224 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6897 (tm-30) REVERT: C 228 LEU cc_start: 0.9466 (pp) cc_final: 0.8991 (pp) REVERT: C 248 PHE cc_start: 0.8946 (m-80) cc_final: 0.8659 (m-10) REVERT: C 368 LYS cc_start: 0.9199 (pttm) cc_final: 0.8831 (pttp) REVERT: D 123 ASN cc_start: 0.8873 (m-40) cc_final: 0.8227 (t0) REVERT: D 124 HIS cc_start: 0.8800 (t-90) cc_final: 0.8555 (t-90) REVERT: D 136 TRP cc_start: 0.8679 (t-100) cc_final: 0.7876 (t60) REVERT: D 158 LEU cc_start: 0.9000 (tp) cc_final: 0.8333 (tt) REVERT: D 159 PHE cc_start: 0.7222 (m-80) cc_final: 0.6032 (m-80) REVERT: D 171 TRP cc_start: 0.7846 (p-90) cc_final: 0.7138 (p-90) REVERT: D 189 CYS cc_start: 0.8847 (m) cc_final: 0.8392 (m) REVERT: D 192 LEU cc_start: 0.9669 (tp) cc_final: 0.9260 (tp) REVERT: D 195 LYS cc_start: 0.9416 (tppt) cc_final: 0.8577 (tppt) REVERT: D 248 PHE cc_start: 0.9193 (m-80) cc_final: 0.8837 (m-10) REVERT: D 283 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8933 (tp40) REVERT: D 328 PHE cc_start: 0.9194 (t80) cc_final: 0.8820 (t80) REVERT: D 329 LYS cc_start: 0.8938 (mttt) cc_final: 0.8603 (mmtt) REVERT: D 330 ILE cc_start: 0.9268 (tt) cc_final: 0.9014 (tt) REVERT: D 358 MET cc_start: 0.8388 (mtm) cc_final: 0.7794 (mtp) REVERT: D 390 LYS cc_start: 0.9065 (mttt) cc_final: 0.8662 (mmtt) REVERT: D 391 LEU cc_start: 0.9615 (mt) cc_final: 0.9327 (mt) REVERT: D 424 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8006 (mt-10) REVERT: E 26 HIS cc_start: 0.6256 (t-90) cc_final: 0.5872 (t70) REVERT: E 27 GLN cc_start: 0.7950 (pt0) cc_final: 0.7710 (pt0) REVERT: E 141 TYR cc_start: 0.8326 (m-80) cc_final: 0.8121 (m-10) REVERT: E 156 THR cc_start: 0.9258 (m) cc_final: 0.9056 (m) REVERT: E 189 CYS cc_start: 0.9238 (t) cc_final: 0.8983 (t) REVERT: E 204 TYR cc_start: 0.8705 (m-80) cc_final: 0.8495 (m-80) REVERT: E 255 GLU cc_start: 0.8494 (pm20) cc_final: 0.8071 (pp20) REVERT: E 304 LYS cc_start: 0.9083 (pptt) cc_final: 0.8789 (pptt) REVERT: E 316 LYS cc_start: 0.8240 (mttt) cc_final: 0.7985 (mttt) REVERT: E 328 PHE cc_start: 0.9016 (t80) cc_final: 0.8390 (t80) REVERT: E 335 LEU cc_start: 0.9042 (mt) cc_final: 0.8599 (mt) REVERT: E 339 MET cc_start: 0.7059 (mtm) cc_final: 0.6579 (mpp) REVERT: E 388 LEU cc_start: 0.9417 (mt) cc_final: 0.9083 (mt) REVERT: F 196 LEU cc_start: 0.8647 (mt) cc_final: 0.8408 (mt) REVERT: F 250 LEU cc_start: 0.9034 (tp) cc_final: 0.8762 (pp) REVERT: F 294 VAL cc_start: 0.7605 (t) cc_final: 0.7275 (t) REVERT: F 328 PHE cc_start: 0.8503 (t80) cc_final: 0.8245 (t80) REVERT: F 332 LEU cc_start: 0.9220 (mt) cc_final: 0.8826 (mt) REVERT: F 339 MET cc_start: 0.8417 (mtt) cc_final: 0.8039 (mpp) REVERT: F 396 HIS cc_start: 0.9111 (t-90) cc_final: 0.8775 (t70) REVERT: F 414 LEU cc_start: 0.9542 (mt) cc_final: 0.9326 (mt) REVERT: P 55 MET cc_start: 0.7453 (tpt) cc_final: 0.5938 (mpp) REVERT: P 67 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7902 (mm-30) REVERT: P 71 GLN cc_start: 0.9229 (mt0) cc_final: 0.8898 (mp10) REVERT: P 74 CYS cc_start: 0.9437 (m) cc_final: 0.9170 (p) REVERT: P 78 LYS cc_start: 0.8834 (mttt) cc_final: 0.8421 (mttt) REVERT: P 139 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8312 (tm-30) REVERT: P 186 CYS cc_start: 0.9490 (m) cc_final: 0.8987 (m) REVERT: P 212 VAL cc_start: 0.9409 (t) cc_final: 0.9053 (m) REVERT: P 225 TRP cc_start: 0.9188 (t-100) cc_final: 0.8838 (t-100) REVERT: P 244 THR cc_start: 0.8444 (p) cc_final: 0.8185 (p) REVERT: P 272 PHE cc_start: 0.8383 (p90) cc_final: 0.8052 (p90) REVERT: P 274 GLU cc_start: 0.5969 (mp0) cc_final: 0.5710 (mp0) REVERT: Q 130 ILE cc_start: 0.9250 (mt) cc_final: 0.8652 (mt) REVERT: Q 131 LEU cc_start: 0.9079 (mt) cc_final: 0.8724 (tp) REVERT: Z 4 GLN cc_start: 0.7125 (mt0) cc_final: 0.6833 (mt0) REVERT: Z 20 VAL cc_start: 0.9721 (p) cc_final: 0.9373 (p) REVERT: Z 24 PHE cc_start: 0.8173 (m-80) cc_final: 0.7395 (m-80) REVERT: Z 26 PHE cc_start: 0.8696 (m-80) cc_final: 0.8455 (m-80) REVERT: Z 75 TRP cc_start: 0.8832 (m-10) cc_final: 0.8512 (m-10) REVERT: Z 117 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6973 (mtp85) REVERT: Z 133 ARG cc_start: 0.9271 (mtm110) cc_final: 0.9032 (mtm110) REVERT: Z 174 PHE cc_start: 0.7747 (m-80) cc_final: 0.6945 (t80) REVERT: Z 192 LYS cc_start: 0.8635 (tttm) cc_final: 0.8277 (tptm) REVERT: Z 194 ASN cc_start: 0.8982 (m-40) cc_final: 0.8430 (p0) REVERT: Z 196 MET cc_start: 0.6432 (tmm) cc_final: 0.5737 (tmm) outliers start: 1 outliers final: 0 residues processed: 641 average time/residue: 0.1325 time to fit residues: 135.5531 Evaluate side-chains 509 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 44 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 278 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 47 GLN Z 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085963 restraints weight = 61666.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088831 restraints weight = 38113.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090795 restraints weight = 26798.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092238 restraints weight = 20708.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093244 restraints weight = 17117.788| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20823 Z= 0.207 Angle : 0.760 10.876 28246 Z= 0.387 Chirality : 0.048 0.276 3359 Planarity : 0.005 0.091 3526 Dihedral : 11.805 174.929 2944 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.15 % Favored : 89.57 % Rotamer: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.16), residues: 2541 helix: -0.34 (0.15), residues: 1162 sheet: -1.67 (0.27), residues: 317 loop : -2.33 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 273 TYR 0.028 0.002 TYR F 204 PHE 0.030 0.002 PHE P 72 TRP 0.043 0.002 TRP P 257 HIS 0.009 0.002 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (20809) covalent geometry : angle 0.75991 / 0.39 (28244) SS BOND : bond 0.00247 / 0.13 ( 1) SS BOND : angle 0.33620 / 0.22 ( 2) hydrogen bonds : bond 0.04206 / 2.83 ( 961) hydrogen bonds : angle 5.59696 / 3.89 ( 2766) Misc. bond : bond 0.00246 / 0.18 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 622 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8803 (m-30) cc_final: 0.8258 (p0) REVERT: A 151 ASP cc_start: 0.8130 (m-30) cc_final: 0.7782 (m-30) REVERT: A 154 MET cc_start: 0.9203 (ttm) cc_final: 0.8952 (ttm) REVERT: A 285 ASP cc_start: 0.9478 (t0) cc_final: 0.9277 (t0) REVERT: A 287 ILE cc_start: 0.8504 (pt) cc_final: 0.8200 (pt) REVERT: A 290 HIS cc_start: 0.8167 (m90) cc_final: 0.7788 (m90) REVERT: A 295 ILE cc_start: 0.9271 (mm) cc_final: 0.9053 (mm) REVERT: A 358 MET cc_start: 0.8337 (mtm) cc_final: 0.8132 (tmm) REVERT: A 377 SER cc_start: 0.7400 (m) cc_final: 0.6812 (t) REVERT: A 391 LEU cc_start: 0.9340 (mt) cc_final: 0.9122 (mt) REVERT: A 399 TYR cc_start: 0.8173 (m-80) cc_final: 0.7882 (m-80) REVERT: B 68 ARG cc_start: 0.9030 (tpt90) cc_final: 0.8672 (tpt90) REVERT: B 123 ASN cc_start: 0.8925 (m-40) cc_final: 0.8530 (m-40) REVERT: B 127 LEU cc_start: 0.9018 (tp) cc_final: 0.8782 (tp) REVERT: B 141 TYR cc_start: 0.6854 (m-10) cc_final: 0.6523 (m-10) REVERT: B 189 CYS cc_start: 0.9152 (m) cc_final: 0.8655 (m) REVERT: B 190 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8986 (mtmm) REVERT: B 231 LYS cc_start: 0.8476 (mttt) cc_final: 0.8242 (tmtt) REVERT: B 248 PHE cc_start: 0.9115 (m-80) cc_final: 0.8811 (m-80) REVERT: B 296 LEU cc_start: 0.9149 (mt) cc_final: 0.8398 (mt) REVERT: B 327 ILE cc_start: 0.9600 (mt) cc_final: 0.9241 (mt) REVERT: B 328 PHE cc_start: 0.9076 (t80) cc_final: 0.8320 (t80) REVERT: B 329 LYS cc_start: 0.9082 (mttt) cc_final: 0.8777 (mmmm) REVERT: B 335 LEU cc_start: 0.9751 (mt) cc_final: 0.9550 (mt) REVERT: B 339 MET cc_start: 0.8611 (mpp) cc_final: 0.8393 (mmt) REVERT: C 23 VAL cc_start: 0.9151 (t) cc_final: 0.8715 (t) REVERT: C 56 TYR cc_start: 0.6943 (t80) cc_final: 0.6736 (m-80) REVERT: C 98 HIS cc_start: 0.6843 (m-70) cc_final: 0.6468 (m90) REVERT: C 200 LEU cc_start: 0.9425 (mm) cc_final: 0.9041 (mm) REVERT: C 212 ILE cc_start: 0.8669 (mm) cc_final: 0.8109 (mm) REVERT: C 224 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6914 (tm-30) REVERT: C 228 LEU cc_start: 0.9486 (pp) cc_final: 0.8999 (pp) REVERT: C 248 PHE cc_start: 0.9022 (m-80) cc_final: 0.8782 (m-10) REVERT: C 253 GLN cc_start: 0.8865 (mt0) cc_final: 0.8194 (mp10) REVERT: C 283 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8947 (mm-40) REVERT: C 368 LYS cc_start: 0.9153 (pttm) cc_final: 0.8833 (pttp) REVERT: D 123 ASN cc_start: 0.8838 (m-40) cc_final: 0.8093 (t0) REVERT: D 136 TRP cc_start: 0.8645 (t-100) cc_final: 0.7872 (t60) REVERT: D 141 TYR cc_start: 0.8887 (m-80) cc_final: 0.8663 (m-80) REVERT: D 158 LEU cc_start: 0.9025 (tp) cc_final: 0.8672 (tp) REVERT: D 159 PHE cc_start: 0.7178 (m-80) cc_final: 0.6606 (m-80) REVERT: D 171 TRP cc_start: 0.8157 (p-90) cc_final: 0.7214 (p-90) REVERT: D 189 CYS cc_start: 0.8822 (m) cc_final: 0.8450 (m) REVERT: D 192 LEU cc_start: 0.9646 (tp) cc_final: 0.9203 (tp) REVERT: D 195 LYS cc_start: 0.9452 (tppt) cc_final: 0.8474 (tppt) REVERT: D 209 LEU cc_start: 0.8128 (tp) cc_final: 0.7921 (tp) REVERT: D 248 PHE cc_start: 0.9180 (m-80) cc_final: 0.8888 (m-10) REVERT: D 274 ILE cc_start: 0.9471 (mm) cc_final: 0.9239 (mm) REVERT: D 278 ASN cc_start: 0.8851 (p0) cc_final: 0.8416 (p0) REVERT: D 296 LEU cc_start: 0.8870 (mt) cc_final: 0.8648 (mt) REVERT: D 317 GLN cc_start: 0.9143 (tp40) cc_final: 0.8925 (tp-100) REVERT: D 328 PHE cc_start: 0.9232 (t80) cc_final: 0.8752 (t80) REVERT: D 329 LYS cc_start: 0.8886 (mttt) cc_final: 0.8574 (mmtt) REVERT: D 330 ILE cc_start: 0.9275 (tt) cc_final: 0.9022 (tt) REVERT: D 351 LEU cc_start: 0.8399 (mt) cc_final: 0.8168 (tp) REVERT: D 358 MET cc_start: 0.8483 (mtm) cc_final: 0.8164 (mtm) REVERT: D 390 LYS cc_start: 0.9174 (mttt) cc_final: 0.8628 (mmtt) REVERT: D 391 LEU cc_start: 0.9611 (mt) cc_final: 0.9324 (mt) REVERT: D 424 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8099 (mt-10) REVERT: E 27 GLN cc_start: 0.7930 (pt0) cc_final: 0.7590 (pt0) REVERT: E 148 HIS cc_start: 0.8543 (m90) cc_final: 0.8168 (m90) REVERT: E 156 THR cc_start: 0.9281 (m) cc_final: 0.9050 (m) REVERT: E 189 CYS cc_start: 0.9356 (t) cc_final: 0.8422 (t) REVERT: E 250 LEU cc_start: 0.9243 (tp) cc_final: 0.8638 (mt) REVERT: E 253 GLN cc_start: 0.8459 (mt0) cc_final: 0.8253 (mt0) REVERT: E 255 GLU cc_start: 0.8421 (pm20) cc_final: 0.8144 (pp20) REVERT: E 278 ASN cc_start: 0.8781 (p0) cc_final: 0.8178 (p0) REVERT: E 316 LYS cc_start: 0.8406 (mttt) cc_final: 0.7952 (mttt) REVERT: E 328 PHE cc_start: 0.9018 (t80) cc_final: 0.8391 (t80) REVERT: E 335 LEU cc_start: 0.9065 (mt) cc_final: 0.8615 (mt) REVERT: E 339 MET cc_start: 0.7145 (mtm) cc_final: 0.6688 (mpp) REVERT: E 388 LEU cc_start: 0.9402 (mt) cc_final: 0.9055 (mt) REVERT: F 196 LEU cc_start: 0.8711 (mt) cc_final: 0.8362 (mt) REVERT: F 250 LEU cc_start: 0.9047 (tp) cc_final: 0.8748 (pp) REVERT: F 294 VAL cc_start: 0.7596 (t) cc_final: 0.7369 (t) REVERT: F 328 PHE cc_start: 0.8552 (t80) cc_final: 0.8299 (t80) REVERT: F 332 LEU cc_start: 0.9187 (mt) cc_final: 0.8985 (mt) REVERT: F 339 MET cc_start: 0.8407 (mtt) cc_final: 0.7971 (mpp) REVERT: F 390 LYS cc_start: 0.9296 (mtpt) cc_final: 0.8960 (mttm) REVERT: F 396 HIS cc_start: 0.9156 (t-90) cc_final: 0.8806 (t70) REVERT: F 414 LEU cc_start: 0.9592 (mt) cc_final: 0.9385 (mt) REVERT: P 55 MET cc_start: 0.7452 (tpt) cc_final: 0.5825 (mpp) REVERT: P 67 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7920 (mm-30) REVERT: P 78 LYS cc_start: 0.8854 (mttt) cc_final: 0.8579 (mttp) REVERT: P 186 CYS cc_start: 0.9441 (m) cc_final: 0.8958 (m) REVERT: P 214 MET cc_start: 0.7948 (mtp) cc_final: 0.7661 (mtp) REVERT: P 225 TRP cc_start: 0.9118 (t-100) cc_final: 0.8752 (t-100) REVERT: P 244 THR cc_start: 0.8532 (p) cc_final: 0.8295 (p) REVERT: Q 130 ILE cc_start: 0.9242 (mt) cc_final: 0.8783 (mt) REVERT: Z 4 GLN cc_start: 0.7147 (mt0) cc_final: 0.6867 (mt0) REVERT: Z 20 VAL cc_start: 0.9694 (p) cc_final: 0.9376 (p) REVERT: Z 24 PHE cc_start: 0.8062 (m-80) cc_final: 0.7349 (m-80) REVERT: Z 26 PHE cc_start: 0.8703 (m-80) cc_final: 0.8313 (m-80) REVERT: Z 75 TRP cc_start: 0.8654 (m-10) cc_final: 0.8448 (m-10) REVERT: Z 133 ARG cc_start: 0.9282 (mtm110) cc_final: 0.8989 (mtm110) REVERT: Z 192 LYS cc_start: 0.8669 (tttm) cc_final: 0.8297 (tptm) REVERT: Z 194 ASN cc_start: 0.8940 (m-40) cc_final: 0.8426 (p0) REVERT: Z 196 MET cc_start: 0.6719 (tmm) cc_final: 0.6136 (tmm) outliers start: 1 outliers final: 1 residues processed: 623 average time/residue: 0.1326 time to fit residues: 131.3516 Evaluate side-chains 495 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 494 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 167 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS D 47 ASN ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086212 restraints weight = 61824.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089105 restraints weight = 38199.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091113 restraints weight = 26788.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092483 restraints weight = 20686.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093486 restraints weight = 17184.990| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20823 Z= 0.204 Angle : 0.761 10.846 28246 Z= 0.390 Chirality : 0.048 0.287 3359 Planarity : 0.005 0.091 3526 Dihedral : 11.698 174.866 2944 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.80 % Favored : 89.93 % Rotamer: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % 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: -1.87 (0.16), residues: 2541 helix: -0.28 (0.15), residues: 1148 sheet: -1.66 (0.26), residues: 342 loop : -2.12 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 354 TYR 0.044 0.002 TYR A 331 PHE 0.029 0.002 PHE P 72 TRP 0.044 0.003 TRP F 136 HIS 0.011 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (20809) covalent geometry : angle 0.76141 / 0.39 (28244) SS BOND : bond 0.00270 / 0.14 ( 1) SS BOND : angle 0.33938 / 0.23 ( 2) hydrogen bonds : bond 0.04206 / 2.86 ( 961) hydrogen bonds : angle 5.57192 / 3.87 ( 2766) Misc. bond : bond 0.00250 / 0.18 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 609 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8734 (m-30) cc_final: 0.8239 (p0) REVERT: A 146 LYS cc_start: 0.9315 (ptpp) cc_final: 0.8981 (pttm) REVERT: A 172 ASN cc_start: 0.8641 (p0) cc_final: 0.8377 (m110) REVERT: A 285 ASP cc_start: 0.9477 (t0) cc_final: 0.9258 (t0) REVERT: A 287 ILE cc_start: 0.8525 (pt) cc_final: 0.8230 (pt) REVERT: A 290 HIS cc_start: 0.8215 (m90) cc_final: 0.7872 (m90) REVERT: A 331 TYR cc_start: 0.8101 (m-80) cc_final: 0.7745 (m-80) REVERT: A 335 LEU cc_start: 0.9462 (mt) cc_final: 0.9260 (mt) REVERT: A 358 MET cc_start: 0.8346 (mtm) cc_final: 0.8136 (tmm) REVERT: A 391 LEU cc_start: 0.9480 (mt) cc_final: 0.9134 (mt) REVERT: A 399 TYR cc_start: 0.8096 (m-80) cc_final: 0.7868 (m-80) REVERT: B 27 GLN cc_start: 0.8329 (tt0) cc_final: 0.8005 (tt0) REVERT: B 68 ARG cc_start: 0.9037 (tpt90) cc_final: 0.8670 (tpt90) REVERT: B 123 ASN cc_start: 0.8895 (m-40) cc_final: 0.8540 (m-40) REVERT: B 127 LEU cc_start: 0.9007 (tp) cc_final: 0.8762 (tp) REVERT: B 141 TYR cc_start: 0.6913 (m-10) cc_final: 0.6650 (m-10) REVERT: B 151 ASP cc_start: 0.8680 (m-30) cc_final: 0.8423 (m-30) REVERT: B 189 CYS cc_start: 0.9131 (m) cc_final: 0.8655 (m) REVERT: B 190 LYS cc_start: 0.9322 (mtmt) cc_final: 0.8967 (mtmm) REVERT: B 231 LYS cc_start: 0.8468 (mttt) cc_final: 0.8214 (tmtt) REVERT: B 248 PHE cc_start: 0.9086 (m-80) cc_final: 0.8782 (m-80) REVERT: B 296 LEU cc_start: 0.9143 (mt) cc_final: 0.8366 (mt) REVERT: B 318 TYR cc_start: 0.9105 (t80) cc_final: 0.8865 (t80) REVERT: B 327 ILE cc_start: 0.9590 (mt) cc_final: 0.9188 (mt) REVERT: B 328 PHE cc_start: 0.9083 (t80) cc_final: 0.8689 (t80) REVERT: B 329 LYS cc_start: 0.9072 (mttt) cc_final: 0.8828 (mmmm) REVERT: B 335 LEU cc_start: 0.9754 (mt) cc_final: 0.9529 (mt) REVERT: B 339 MET cc_start: 0.8613 (mpp) cc_final: 0.8288 (mmm) REVERT: B 424 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7974 (mt-10) REVERT: C 23 VAL cc_start: 0.9140 (t) cc_final: 0.8784 (t) REVERT: C 98 HIS cc_start: 0.6740 (m-70) cc_final: 0.6429 (m90) REVERT: C 185 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9162 (ttmt) REVERT: C 189 CYS cc_start: 0.8888 (m) cc_final: 0.8609 (m) REVERT: C 212 ILE cc_start: 0.8723 (mm) cc_final: 0.8065 (mm) REVERT: C 224 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6932 (tm-30) REVERT: C 228 LEU cc_start: 0.9443 (pp) cc_final: 0.8868 (pp) REVERT: C 368 LYS cc_start: 0.9214 (pttm) cc_final: 0.8847 (pttp) REVERT: D 136 TRP cc_start: 0.8642 (t-100) cc_final: 0.7883 (t60) REVERT: D 141 TYR cc_start: 0.8891 (m-80) cc_final: 0.8671 (m-80) REVERT: D 158 LEU cc_start: 0.9023 (tp) cc_final: 0.8703 (tp) REVERT: D 159 PHE cc_start: 0.7165 (m-80) cc_final: 0.6389 (m-80) REVERT: D 171 TRP cc_start: 0.8138 (p-90) cc_final: 0.7028 (p-90) REVERT: D 189 CYS cc_start: 0.8794 (m) cc_final: 0.8466 (m) REVERT: D 190 LYS cc_start: 0.9415 (mttt) cc_final: 0.8568 (mmmm) REVERT: D 192 LEU cc_start: 0.9640 (tp) cc_final: 0.9248 (tp) REVERT: D 195 LYS cc_start: 0.9431 (tppt) cc_final: 0.8285 (tppt) REVERT: D 209 LEU cc_start: 0.8362 (tp) cc_final: 0.7657 (tp) REVERT: D 248 PHE cc_start: 0.9230 (m-80) cc_final: 0.8751 (m-10) REVERT: D 278 ASN cc_start: 0.9047 (p0) cc_final: 0.8684 (p0) REVERT: D 296 LEU cc_start: 0.8843 (mt) cc_final: 0.8599 (mt) REVERT: D 298 THR cc_start: 0.8985 (p) cc_final: 0.8763 (p) REVERT: D 306 ASP cc_start: 0.8281 (t0) cc_final: 0.7867 (p0) REVERT: D 316 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8121 (mtpt) REVERT: D 328 PHE cc_start: 0.9235 (t80) cc_final: 0.8803 (t80) REVERT: D 329 LYS cc_start: 0.8917 (mttt) cc_final: 0.8607 (mmtt) REVERT: D 351 LEU cc_start: 0.8476 (mt) cc_final: 0.8213 (tp) REVERT: D 358 MET cc_start: 0.8551 (mtm) cc_final: 0.8191 (mtm) REVERT: D 391 LEU cc_start: 0.9620 (mt) cc_final: 0.9333 (mt) REVERT: D 424 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7979 (mt-10) REVERT: E 27 GLN cc_start: 0.7990 (pt0) cc_final: 0.7654 (pt0) REVERT: E 168 LEU cc_start: 0.9388 (mp) cc_final: 0.8352 (tt) REVERT: E 253 GLN cc_start: 0.8525 (mt0) cc_final: 0.8208 (mt0) REVERT: E 314 ASP cc_start: 0.8473 (m-30) cc_final: 0.8223 (m-30) REVERT: E 316 LYS cc_start: 0.8502 (mttt) cc_final: 0.8046 (mttt) REVERT: E 328 PHE cc_start: 0.9028 (t80) cc_final: 0.8394 (t80) REVERT: E 335 LEU cc_start: 0.9069 (mt) cc_final: 0.8617 (mt) REVERT: E 339 MET cc_start: 0.6994 (mtm) cc_final: 0.6571 (mpp) REVERT: E 388 LEU cc_start: 0.9393 (mt) cc_final: 0.9045 (mt) REVERT: F 136 TRP cc_start: 0.7761 (t-100) cc_final: 0.7395 (t-100) REVERT: F 196 LEU cc_start: 0.8729 (mt) cc_final: 0.8455 (mt) REVERT: F 250 LEU cc_start: 0.9048 (tp) cc_final: 0.8735 (pp) REVERT: F 294 VAL cc_start: 0.7596 (t) cc_final: 0.7379 (t) REVERT: F 328 PHE cc_start: 0.8544 (t80) cc_final: 0.8243 (t80) REVERT: F 332 LEU cc_start: 0.9188 (mt) cc_final: 0.8972 (mt) REVERT: F 338 LEU cc_start: 0.8951 (mt) cc_final: 0.8730 (mt) REVERT: F 339 MET cc_start: 0.8402 (mtt) cc_final: 0.7951 (mpp) REVERT: F 396 HIS cc_start: 0.9074 (t-90) cc_final: 0.8767 (t70) REVERT: P 55 MET cc_start: 0.7594 (tpt) cc_final: 0.5840 (mpp) REVERT: P 78 LYS cc_start: 0.8830 (mttt) cc_final: 0.8539 (mttp) REVERT: P 186 CYS cc_start: 0.9534 (m) cc_final: 0.9161 (m) REVERT: P 225 TRP cc_start: 0.9127 (t-100) cc_final: 0.8772 (t-100) REVERT: P 244 THR cc_start: 0.8508 (p) cc_final: 0.8255 (p) REVERT: Q 130 ILE cc_start: 0.8993 (mt) cc_final: 0.8687 (mt) REVERT: Z 4 GLN cc_start: 0.7040 (mt0) cc_final: 0.6722 (mt0) REVERT: Z 20 VAL cc_start: 0.9661 (p) cc_final: 0.9412 (p) REVERT: Z 24 PHE cc_start: 0.8038 (m-80) cc_final: 0.7443 (m-80) REVERT: Z 26 PHE cc_start: 0.8685 (m-80) cc_final: 0.8478 (m-80) REVERT: Z 33 TYR cc_start: 0.8802 (t80) cc_final: 0.8429 (t80) REVERT: Z 75 TRP cc_start: 0.8648 (m-10) cc_final: 0.8432 (m-10) REVERT: Z 133 ARG cc_start: 0.9267 (mtm110) cc_final: 0.8937 (mtm110) REVERT: Z 192 LYS cc_start: 0.8678 (tttm) cc_final: 0.8326 (tptm) REVERT: Z 194 ASN cc_start: 0.8935 (m-40) cc_final: 0.8431 (p0) REVERT: Z 196 MET cc_start: 0.6783 (tmm) cc_final: 0.6223 (tmm) outliers start: 1 outliers final: 0 residues processed: 609 average time/residue: 0.1275 time to fit residues: 124.5356 Evaluate side-chains 483 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 158 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 212 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 13 optimal weight: 0.0970 chunk 90 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 175 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 HIS ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 264 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090098 restraints weight = 60111.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093166 restraints weight = 37055.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.095313 restraints weight = 25939.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096767 restraints weight = 19894.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097898 restraints weight = 16467.358| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20823 Z= 0.142 Angle : 0.730 10.427 28246 Z= 0.374 Chirality : 0.049 0.327 3359 Planarity : 0.005 0.087 3526 Dihedral : 11.463 175.466 2944 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 0.05 % Allowed : 1.27 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.12 % 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: -1.57 (0.17), residues: 2541 helix: -0.08 (0.15), residues: 1166 sheet: -1.43 (0.27), residues: 351 loop : -1.96 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 205 TYR 0.038 0.002 TYR A 331 PHE 0.025 0.002 PHE P 72 TRP 0.064 0.003 TRP P 257 HIS 0.012 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (20809) covalent geometry : angle 0.73039 / 0.37 (28244) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 0.45556 / 0.30 ( 2) hydrogen bonds : bond 0.03918 / 2.66 ( 961) hydrogen bonds : angle 5.31685 / 3.72 ( 2766) Misc. bond : bond 0.00235 / 0.17 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 650 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8652 (m-30) cc_final: 0.8181 (p0) REVERT: A 154 MET cc_start: 0.8996 (ttp) cc_final: 0.8782 (ptm) REVERT: A 172 ASN cc_start: 0.8657 (p0) cc_final: 0.8360 (m110) REVERT: A 285 ASP cc_start: 0.9459 (t0) cc_final: 0.9233 (t0) REVERT: A 287 ILE cc_start: 0.8460 (pt) cc_final: 0.8096 (pt) REVERT: A 290 HIS cc_start: 0.8392 (m90) cc_final: 0.8066 (m90) REVERT: A 327 ILE cc_start: 0.9538 (mt) cc_final: 0.9134 (mt) REVERT: A 331 TYR cc_start: 0.8406 (m-80) cc_final: 0.7676 (m-80) REVERT: A 335 LEU cc_start: 0.9470 (mt) cc_final: 0.9249 (mt) REVERT: A 358 MET cc_start: 0.8214 (mtm) cc_final: 0.8003 (tmm) REVERT: A 391 LEU cc_start: 0.9409 (mt) cc_final: 0.9114 (mt) REVERT: A 399 TYR cc_start: 0.8015 (m-80) cc_final: 0.7773 (m-80) REVERT: B 27 GLN cc_start: 0.8199 (tt0) cc_final: 0.7882 (tt0) REVERT: B 68 ARG cc_start: 0.9041 (tpt90) cc_final: 0.8703 (tpt90) REVERT: B 123 ASN cc_start: 0.8989 (m-40) cc_final: 0.8674 (m-40) REVERT: B 127 LEU cc_start: 0.8973 (tp) cc_final: 0.8691 (tp) REVERT: B 141 TYR cc_start: 0.7319 (m-10) cc_final: 0.6805 (m-10) REVERT: B 151 ASP cc_start: 0.8637 (m-30) cc_final: 0.8317 (m-30) REVERT: B 189 CYS cc_start: 0.9133 (m) cc_final: 0.8718 (m) REVERT: B 190 LYS cc_start: 0.9279 (mtmt) cc_final: 0.8937 (mtmm) REVERT: B 231 LYS cc_start: 0.8394 (mttt) cc_final: 0.8097 (tmtt) REVERT: B 248 PHE cc_start: 0.9173 (m-80) cc_final: 0.8653 (m-80) REVERT: B 281 LEU cc_start: 0.9619 (mp) cc_final: 0.9404 (mp) REVERT: B 296 LEU cc_start: 0.9126 (mt) cc_final: 0.8544 (mt) REVERT: B 328 PHE cc_start: 0.9048 (t80) cc_final: 0.8389 (t80) REVERT: B 329 LYS cc_start: 0.9003 (mttt) cc_final: 0.8677 (mmmm) REVERT: B 335 LEU cc_start: 0.9714 (mt) cc_final: 0.9428 (mt) REVERT: B 339 MET cc_start: 0.8605 (mpp) cc_final: 0.8292 (mmm) REVERT: B 424 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7435 (pt0) REVERT: C 23 VAL cc_start: 0.9045 (t) cc_final: 0.8720 (t) REVERT: C 98 HIS cc_start: 0.6565 (m-70) cc_final: 0.6308 (m90) REVERT: C 189 CYS cc_start: 0.9065 (m) cc_final: 0.8784 (m) REVERT: C 212 ILE cc_start: 0.8530 (mm) cc_final: 0.7849 (mm) REVERT: C 224 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6701 (tm-30) REVERT: C 228 LEU cc_start: 0.9433 (pp) cc_final: 0.8805 (pp) REVERT: C 255 GLU cc_start: 0.9356 (mp0) cc_final: 0.9106 (mp0) REVERT: C 283 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8544 (mm110) REVERT: C 316 LYS cc_start: 0.8113 (tttt) cc_final: 0.7717 (tttt) REVERT: C 347 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8024 (mmp80) REVERT: C 368 LYS cc_start: 0.9199 (pttm) cc_final: 0.8824 (pttp) REVERT: D 136 TRP cc_start: 0.8582 (t-100) cc_final: 0.7739 (t60) REVERT: D 158 LEU cc_start: 0.8974 (tp) cc_final: 0.8628 (tp) REVERT: D 159 PHE cc_start: 0.6970 (m-80) cc_final: 0.6350 (m-80) REVERT: D 171 TRP cc_start: 0.7723 (p-90) cc_final: 0.6407 (p-90) REVERT: D 189 CYS cc_start: 0.8886 (m) cc_final: 0.8493 (m) REVERT: D 190 LYS cc_start: 0.9318 (mttt) cc_final: 0.8455 (mmmm) REVERT: D 192 LEU cc_start: 0.9680 (tp) cc_final: 0.9272 (tp) REVERT: D 195 LYS cc_start: 0.9400 (tppt) cc_final: 0.8272 (tppt) REVERT: D 209 LEU cc_start: 0.8051 (tp) cc_final: 0.7586 (tp) REVERT: D 248 PHE cc_start: 0.9063 (m-80) cc_final: 0.8747 (m-10) REVERT: D 255 GLU cc_start: 0.8819 (pt0) cc_final: 0.6537 (tp30) REVERT: D 296 LEU cc_start: 0.8820 (mt) cc_final: 0.7588 (mt) REVERT: D 306 ASP cc_start: 0.8286 (t0) cc_final: 0.7787 (p0) REVERT: D 316 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8077 (mtpt) REVERT: D 358 MET cc_start: 0.8557 (mtm) cc_final: 0.8195 (mtm) REVERT: D 390 LYS cc_start: 0.9240 (mttt) cc_final: 0.8980 (mttp) REVERT: D 391 LEU cc_start: 0.9557 (mt) cc_final: 0.9315 (mt) REVERT: D 424 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7791 (mt-10) REVERT: E 24 GLU cc_start: 0.7933 (pp20) cc_final: 0.7724 (pp20) REVERT: E 27 GLN cc_start: 0.7930 (pt0) cc_final: 0.7498 (pt0) REVERT: E 154 MET cc_start: 0.9129 (ttm) cc_final: 0.8883 (ttm) REVERT: E 168 LEU cc_start: 0.9423 (mp) cc_final: 0.8335 (tt) REVERT: E 189 CYS cc_start: 0.9340 (t) cc_final: 0.8997 (t) REVERT: E 252 ASP cc_start: 0.6862 (t0) cc_final: 0.6602 (t0) REVERT: E 316 LYS cc_start: 0.8469 (mttt) cc_final: 0.7896 (mttt) REVERT: E 328 PHE cc_start: 0.9007 (t80) cc_final: 0.8409 (t80) REVERT: E 339 MET cc_start: 0.6996 (mtm) cc_final: 0.6603 (mtp) REVERT: E 375 ASP cc_start: 0.8761 (m-30) cc_final: 0.7931 (t70) REVERT: E 388 LEU cc_start: 0.9471 (mt) cc_final: 0.9118 (mt) REVERT: F 196 LEU cc_start: 0.8662 (mt) cc_final: 0.8268 (mt) REVERT: F 250 LEU cc_start: 0.8983 (tp) cc_final: 0.8703 (pp) REVERT: F 275 ARG cc_start: 0.8214 (mmp80) cc_final: 0.7924 (tmm160) REVERT: F 294 VAL cc_start: 0.7527 (t) cc_final: 0.7280 (t) REVERT: F 328 PHE cc_start: 0.8420 (t80) cc_final: 0.8116 (t80) REVERT: F 338 LEU cc_start: 0.8880 (mt) cc_final: 0.8645 (mt) REVERT: F 339 MET cc_start: 0.8239 (mtt) cc_final: 0.7825 (mpp) REVERT: F 390 LYS cc_start: 0.9454 (mttt) cc_final: 0.9143 (mttm) REVERT: F 396 HIS cc_start: 0.9122 (t-90) cc_final: 0.8767 (t-170) REVERT: P 55 MET cc_start: 0.7716 (tpt) cc_final: 0.5897 (mpp) REVERT: P 78 LYS cc_start: 0.8761 (mttt) cc_final: 0.8472 (mttp) REVERT: P 186 CYS cc_start: 0.9531 (m) cc_final: 0.9153 (m) REVERT: P 223 GLU cc_start: 0.8627 (tp30) cc_final: 0.7762 (tm-30) REVERT: P 225 TRP cc_start: 0.9067 (t-100) cc_final: 0.8823 (t-100) REVERT: P 240 LYS cc_start: 0.7514 (mmmm) cc_final: 0.7071 (tttt) REVERT: P 272 PHE cc_start: 0.8005 (p90) cc_final: 0.7748 (p90) REVERT: P 274 GLU cc_start: 0.6496 (mp0) cc_final: 0.5955 (mp0) REVERT: Q 130 ILE cc_start: 0.9023 (mt) cc_final: 0.8737 (mt) REVERT: Z 20 VAL cc_start: 0.9630 (p) cc_final: 0.9404 (p) REVERT: Z 24 PHE cc_start: 0.7923 (m-80) cc_final: 0.7338 (m-80) REVERT: Z 33 TYR cc_start: 0.8776 (t80) cc_final: 0.8196 (t80) REVERT: Z 70 GLU cc_start: 0.9079 (mp0) cc_final: 0.8841 (mp0) REVERT: Z 75 TRP cc_start: 0.8619 (m-10) cc_final: 0.8334 (m-10) REVERT: Z 183 LEU cc_start: 0.8914 (mp) cc_final: 0.8411 (mp) REVERT: Z 194 ASN cc_start: 0.8900 (m-40) cc_final: 0.8526 (p0) REVERT: Z 195 SER cc_start: 0.8195 (m) cc_final: 0.7193 (t) REVERT: Z 196 MET cc_start: 0.6741 (tmm) cc_final: 0.5847 (tmm) outliers start: 1 outliers final: 1 residues processed: 651 average time/residue: 0.1252 time to fit residues: 130.1797 Evaluate side-chains 520 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 519 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 169 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 176 optimal weight: 0.3980 chunk 237 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 264 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.113700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087929 restraints weight = 60722.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090768 restraints weight = 37719.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092802 restraints weight = 26665.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094225 restraints weight = 20528.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.095145 restraints weight = 16964.418| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20823 Z= 0.192 Angle : 0.766 10.032 28246 Z= 0.392 Chirality : 0.049 0.272 3359 Planarity : 0.005 0.089 3526 Dihedral : 11.495 175.395 2944 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.25 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.16 % 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: -1.59 (0.17), residues: 2541 helix: -0.13 (0.15), residues: 1160 sheet: -1.34 (0.28), residues: 347 loop : -1.97 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 203 TYR 0.039 0.002 TYR A 331 PHE 0.025 0.002 PHE P 142 TRP 0.060 0.003 TRP P 257 HIS 0.014 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (20809) covalent geometry : angle 0.76601 / 0.39 (28244) SS BOND : bond 0.00201 / 0.11 ( 1) SS BOND : angle 0.21799 / 0.15 ( 2) hydrogen bonds : bond 0.04078 / 2.75 ( 961) hydrogen bonds : angle 5.52443 / 3.89 ( 2766) Misc. bond : bond 0.00230 / 0.17 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8703 (m-30) cc_final: 0.8234 (p0) REVERT: A 150 LEU cc_start: 0.9260 (tp) cc_final: 0.8681 (tp) REVERT: A 154 MET cc_start: 0.8983 (ttp) cc_final: 0.8648 (ptm) REVERT: A 172 ASN cc_start: 0.8699 (p0) cc_final: 0.8404 (m110) REVERT: A 285 ASP cc_start: 0.9462 (t0) cc_final: 0.9214 (t0) REVERT: A 287 ILE cc_start: 0.8492 (pt) cc_final: 0.8273 (pt) REVERT: A 290 HIS cc_start: 0.8415 (m90) cc_final: 0.8118 (m90) REVERT: A 327 ILE cc_start: 0.9564 (mt) cc_final: 0.9073 (mt) REVERT: A 331 TYR cc_start: 0.8603 (m-80) cc_final: 0.7785 (m-80) REVERT: A 335 LEU cc_start: 0.9467 (mt) cc_final: 0.9247 (mt) REVERT: A 356 LEU cc_start: 0.9531 (mt) cc_final: 0.9130 (tp) REVERT: A 358 MET cc_start: 0.8231 (mtm) cc_final: 0.8006 (tmm) REVERT: A 390 LYS cc_start: 0.8694 (tptp) cc_final: 0.7989 (tptp) REVERT: A 391 LEU cc_start: 0.9450 (mt) cc_final: 0.9127 (mt) REVERT: A 399 TYR cc_start: 0.8035 (m-80) cc_final: 0.7776 (m-80) REVERT: B 27 GLN cc_start: 0.8250 (tt0) cc_final: 0.7955 (tt0) REVERT: B 68 ARG cc_start: 0.9020 (tpt90) cc_final: 0.8695 (tpt90) REVERT: B 123 ASN cc_start: 0.9018 (m-40) cc_final: 0.8728 (m-40) REVERT: B 151 ASP cc_start: 0.8687 (m-30) cc_final: 0.8366 (m-30) REVERT: B 189 CYS cc_start: 0.9159 (m) cc_final: 0.8819 (m) REVERT: B 190 LYS cc_start: 0.9357 (mtmt) cc_final: 0.8986 (mtmm) REVERT: B 231 LYS cc_start: 0.8470 (mttt) cc_final: 0.8136 (tmtt) REVERT: B 248 PHE cc_start: 0.9104 (m-80) cc_final: 0.8819 (m-80) REVERT: B 296 LEU cc_start: 0.9192 (mt) cc_final: 0.8487 (mt) REVERT: B 327 ILE cc_start: 0.9526 (mt) cc_final: 0.9163 (mt) REVERT: B 328 PHE cc_start: 0.9135 (t80) cc_final: 0.8345 (t80) REVERT: B 329 LYS cc_start: 0.9066 (mttt) cc_final: 0.8801 (mmmm) REVERT: B 335 LEU cc_start: 0.9734 (mt) cc_final: 0.9380 (mt) REVERT: B 339 MET cc_start: 0.8615 (mpp) cc_final: 0.8250 (mmm) REVERT: B 424 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8008 (mt-10) REVERT: C 23 VAL cc_start: 0.9016 (t) cc_final: 0.8678 (t) REVERT: C 98 HIS cc_start: 0.6621 (m-70) cc_final: 0.6353 (m90) REVERT: C 212 ILE cc_start: 0.8321 (mm) cc_final: 0.7623 (mm) REVERT: C 224 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7072 (tm-30) REVERT: C 228 LEU cc_start: 0.9437 (pp) cc_final: 0.8878 (pp) REVERT: C 331 TYR cc_start: 0.9101 (m-10) cc_final: 0.8820 (m-80) REVERT: C 347 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7954 (mmp80) REVERT: C 368 LYS cc_start: 0.9217 (pttm) cc_final: 0.8856 (pttp) REVERT: D 136 TRP cc_start: 0.8603 (t-100) cc_final: 0.7849 (t60) REVERT: D 158 LEU cc_start: 0.9027 (tp) cc_final: 0.8704 (tp) REVERT: D 159 PHE cc_start: 0.7401 (m-80) cc_final: 0.6566 (m-80) REVERT: D 171 TRP cc_start: 0.7960 (p-90) cc_final: 0.6488 (p-90) REVERT: D 189 CYS cc_start: 0.8932 (m) cc_final: 0.8629 (m) REVERT: D 190 LYS cc_start: 0.9368 (mttt) cc_final: 0.8472 (mmmm) REVERT: D 192 LEU cc_start: 0.9639 (tp) cc_final: 0.9261 (tp) REVERT: D 195 LYS cc_start: 0.9558 (tppt) cc_final: 0.8281 (tppt) REVERT: D 209 LEU cc_start: 0.8174 (tp) cc_final: 0.7927 (tp) REVERT: D 248 PHE cc_start: 0.9114 (m-80) cc_final: 0.8685 (m-10) REVERT: D 255 GLU cc_start: 0.9038 (pt0) cc_final: 0.7590 (tt0) REVERT: D 296 LEU cc_start: 0.8829 (mt) cc_final: 0.7530 (mt) REVERT: D 306 ASP cc_start: 0.8217 (t0) cc_final: 0.7700 (p0) REVERT: D 316 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8101 (mtpt) REVERT: D 339 MET cc_start: 0.7850 (tpp) cc_final: 0.7458 (tpp) REVERT: D 376 ILE cc_start: 0.9447 (mm) cc_final: 0.9164 (mm) REVERT: D 391 LEU cc_start: 0.9611 (mt) cc_final: 0.9344 (mt) REVERT: D 424 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7797 (mt-10) REVERT: E 27 GLN cc_start: 0.7952 (pt0) cc_final: 0.7609 (pt0) REVERT: E 133 HIS cc_start: 0.7826 (t70) cc_final: 0.7067 (t70) REVERT: E 148 HIS cc_start: 0.8524 (m90) cc_final: 0.8303 (m90) REVERT: E 154 MET cc_start: 0.9142 (ttm) cc_final: 0.8935 (ttm) REVERT: E 189 CYS cc_start: 0.9317 (t) cc_final: 0.8991 (t) REVERT: E 252 ASP cc_start: 0.6876 (t0) cc_final: 0.6612 (t0) REVERT: E 283 GLN cc_start: 0.9252 (mp10) cc_final: 0.8855 (mp10) REVERT: E 316 LYS cc_start: 0.8546 (mttt) cc_final: 0.7972 (mttt) REVERT: E 335 LEU cc_start: 0.9093 (mt) cc_final: 0.8871 (mt) REVERT: E 375 ASP cc_start: 0.8772 (m-30) cc_final: 0.7959 (t70) REVERT: E 388 LEU cc_start: 0.9447 (mt) cc_final: 0.9065 (mt) REVERT: F 136 TRP cc_start: 0.7837 (t-100) cc_final: 0.7354 (t-100) REVERT: F 250 LEU cc_start: 0.9002 (tp) cc_final: 0.8667 (pp) REVERT: F 275 ARG cc_start: 0.8332 (mmp80) cc_final: 0.7986 (tmm160) REVERT: F 294 VAL cc_start: 0.7534 (t) cc_final: 0.7305 (t) REVERT: F 328 PHE cc_start: 0.8507 (t80) cc_final: 0.8181 (t80) REVERT: F 338 LEU cc_start: 0.8911 (mt) cc_final: 0.8688 (mt) REVERT: F 339 MET cc_start: 0.8115 (mtt) cc_final: 0.7676 (mpp) REVERT: F 390 LYS cc_start: 0.9471 (mttt) cc_final: 0.9187 (mttm) REVERT: P 55 MET cc_start: 0.7644 (tpt) cc_final: 0.5913 (mpp) REVERT: P 78 LYS cc_start: 0.8814 (mttt) cc_final: 0.8574 (mttp) REVERT: P 186 CYS cc_start: 0.9478 (m) cc_final: 0.8914 (p) REVERT: P 225 TRP cc_start: 0.9084 (t-100) cc_final: 0.8734 (t-100) REVERT: P 240 LYS cc_start: 0.7588 (mmmm) cc_final: 0.7202 (tttt) REVERT: P 272 PHE cc_start: 0.8101 (p90) cc_final: 0.7831 (p90) REVERT: P 274 GLU cc_start: 0.6437 (mp0) cc_final: 0.6047 (mp0) REVERT: Q 130 ILE cc_start: 0.9178 (mt) cc_final: 0.8824 (mt) REVERT: Z 24 PHE cc_start: 0.7850 (m-80) cc_final: 0.7381 (m-80) REVERT: Z 33 TYR cc_start: 0.8801 (t80) cc_final: 0.8201 (t80) REVERT: Z 49 TYR cc_start: 0.6873 (m-80) cc_final: 0.6330 (m-80) REVERT: Z 70 GLU cc_start: 0.9267 (mp0) cc_final: 0.8736 (mp0) REVERT: Z 75 TRP cc_start: 0.8618 (m-10) cc_final: 0.8367 (m-10) REVERT: Z 192 LYS cc_start: 0.8369 (tttm) cc_final: 0.8028 (tptm) REVERT: Z 194 ASN cc_start: 0.8808 (m-40) cc_final: 0.8351 (p0) REVERT: Z 196 MET cc_start: 0.6828 (tmm) cc_final: 0.6042 (tmm) outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 0.1312 time to fit residues: 128.3129 Evaluate side-chains 495 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 222 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 75 optimal weight: 30.0000 chunk 112 optimal weight: 0.0470 chunk 223 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 396 HIS D 27 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 412 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 264 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.117088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090546 restraints weight = 60156.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093640 restraints weight = 36927.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095753 restraints weight = 25755.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097289 restraints weight = 19794.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098323 restraints weight = 16268.553| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20823 Z= 0.148 Angle : 0.745 11.525 28246 Z= 0.379 Chirality : 0.049 0.256 3359 Planarity : 0.005 0.091 3526 Dihedral : 11.420 176.719 2944 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.83 % Favored : 91.97 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.08 % 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: -1.41 (0.17), residues: 2541 helix: -0.03 (0.15), residues: 1152 sheet: -1.22 (0.28), residues: 349 loop : -1.80 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 203 TYR 0.037 0.002 TYR A 331 PHE 0.027 0.002 PHE B 218 TRP 0.029 0.002 TRP F 136 HIS 0.015 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (20809) covalent geometry : angle 0.74524 / 0.38 (28244) SS BOND : bond 0.00099 / 0.05 ( 1) SS BOND : angle 0.40908 / 0.27 ( 2) hydrogen bonds : bond 0.03852 / 2.59 ( 961) hydrogen bonds : angle 5.41009 / 3.80 ( 2766) Misc. bond : bond 0.00226 / 0.17 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 629 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8647 (m-30) cc_final: 0.8202 (p0) REVERT: A 150 LEU cc_start: 0.9190 (tp) cc_final: 0.8611 (tp) REVERT: A 154 MET cc_start: 0.8910 (ttp) cc_final: 0.8534 (ptm) REVERT: A 172 ASN cc_start: 0.8686 (p0) cc_final: 0.8413 (m110) REVERT: A 173 ARG cc_start: 0.7918 (mtt90) cc_final: 0.6555 (mpt-90) REVERT: A 285 ASP cc_start: 0.9484 (t0) cc_final: 0.8949 (t0) REVERT: A 287 ILE cc_start: 0.8552 (pt) cc_final: 0.8168 (pt) REVERT: A 290 HIS cc_start: 0.8328 (m90) cc_final: 0.7868 (m90) REVERT: A 328 PHE cc_start: 0.8996 (t80) cc_final: 0.8781 (t80) REVERT: A 331 TYR cc_start: 0.8637 (m-80) cc_final: 0.7706 (m-80) REVERT: A 335 LEU cc_start: 0.9475 (mt) cc_final: 0.9261 (mt) REVERT: A 356 LEU cc_start: 0.9495 (mt) cc_final: 0.9063 (tp) REVERT: A 358 MET cc_start: 0.8245 (mtm) cc_final: 0.7996 (tmm) REVERT: A 390 LYS cc_start: 0.8730 (tptp) cc_final: 0.8043 (tptp) REVERT: A 391 LEU cc_start: 0.9350 (mt) cc_final: 0.9044 (mt) REVERT: A 399 TYR cc_start: 0.7949 (m-80) cc_final: 0.7738 (m-80) REVERT: B 27 GLN cc_start: 0.8156 (tt0) cc_final: 0.7849 (tt0) REVERT: B 68 ARG cc_start: 0.9035 (tpt90) cc_final: 0.8698 (tpt90) REVERT: B 123 ASN cc_start: 0.8953 (m-40) cc_final: 0.8064 (m-40) REVERT: B 190 LYS cc_start: 0.9345 (mtmt) cc_final: 0.8965 (mtmm) REVERT: B 211 GLU cc_start: 0.8400 (tt0) cc_final: 0.8172 (tt0) REVERT: B 231 LYS cc_start: 0.8430 (mttt) cc_final: 0.8103 (tmtt) REVERT: B 248 PHE cc_start: 0.9029 (m-80) cc_final: 0.8649 (m-80) REVERT: B 296 LEU cc_start: 0.9104 (mt) cc_final: 0.8075 (mt) REVERT: B 328 PHE cc_start: 0.9103 (t80) cc_final: 0.8286 (t80) REVERT: B 329 LYS cc_start: 0.9049 (mttt) cc_final: 0.8748 (mmmm) REVERT: B 335 LEU cc_start: 0.9706 (mt) cc_final: 0.9408 (mt) REVERT: B 339 MET cc_start: 0.8580 (mpp) cc_final: 0.8244 (mmm) REVERT: B 416 LEU cc_start: 0.9013 (mm) cc_final: 0.8761 (mm) REVERT: B 419 ASP cc_start: 0.9079 (m-30) cc_final: 0.8570 (m-30) REVERT: B 424 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7566 (pt0) REVERT: C 98 HIS cc_start: 0.6580 (m-70) cc_final: 0.6327 (m90) REVERT: C 176 LEU cc_start: 0.8883 (tp) cc_final: 0.8298 (tt) REVERT: C 188 LEU cc_start: 0.9146 (tt) cc_final: 0.8898 (tt) REVERT: C 189 CYS cc_start: 0.9073 (m) cc_final: 0.8855 (m) REVERT: C 224 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6733 (tm-30) REVERT: C 228 LEU cc_start: 0.9410 (pp) cc_final: 0.8688 (pp) REVERT: C 316 LYS cc_start: 0.8109 (tttt) cc_final: 0.7758 (tttt) REVERT: C 331 TYR cc_start: 0.8989 (m-10) cc_final: 0.8734 (m-80) REVERT: C 347 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7807 (mmm160) REVERT: C 368 LYS cc_start: 0.9215 (pttm) cc_final: 0.8828 (pttp) REVERT: D 124 HIS cc_start: 0.9092 (t-90) cc_final: 0.8786 (t-90) REVERT: D 136 TRP cc_start: 0.8500 (t-100) cc_final: 0.7744 (t60) REVERT: D 158 LEU cc_start: 0.9006 (tp) cc_final: 0.8409 (tt) REVERT: D 159 PHE cc_start: 0.6961 (m-80) cc_final: 0.5899 (m-80) REVERT: D 171 TRP cc_start: 0.7779 (p-90) cc_final: 0.6485 (p-90) REVERT: D 189 CYS cc_start: 0.8937 (m) cc_final: 0.8587 (m) REVERT: D 192 LEU cc_start: 0.9640 (tp) cc_final: 0.9259 (tp) REVERT: D 195 LYS cc_start: 0.9558 (tppt) cc_final: 0.8289 (tppt) REVERT: D 274 ILE cc_start: 0.9372 (mm) cc_final: 0.9085 (mm) REVERT: D 296 LEU cc_start: 0.8915 (mt) cc_final: 0.7756 (mt) REVERT: D 306 ASP cc_start: 0.8340 (t0) cc_final: 0.7911 (p0) REVERT: D 316 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8042 (mtpt) REVERT: D 351 LEU cc_start: 0.8385 (tp) cc_final: 0.8087 (tp) REVERT: D 391 LEU cc_start: 0.9548 (mt) cc_final: 0.9277 (mt) REVERT: E 27 GLN cc_start: 0.7888 (pt0) cc_final: 0.7531 (pt0) REVERT: E 28 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7256 (mmm-85) REVERT: E 154 MET cc_start: 0.9241 (ttm) cc_final: 0.9011 (ttm) REVERT: E 189 CYS cc_start: 0.9332 (t) cc_final: 0.9079 (t) REVERT: E 252 ASP cc_start: 0.6811 (t0) cc_final: 0.6582 (t0) REVERT: E 257 LEU cc_start: 0.8888 (mt) cc_final: 0.8617 (mp) REVERT: E 316 LYS cc_start: 0.8324 (mttt) cc_final: 0.7892 (mttt) REVERT: E 375 ASP cc_start: 0.8803 (m-30) cc_final: 0.8069 (t70) REVERT: E 388 LEU cc_start: 0.9460 (mt) cc_final: 0.9104 (mt) REVERT: F 196 LEU cc_start: 0.8862 (mt) cc_final: 0.8652 (mt) REVERT: F 250 LEU cc_start: 0.8866 (tp) cc_final: 0.8605 (pp) REVERT: F 275 ARG cc_start: 0.8375 (mmp80) cc_final: 0.8024 (tmm160) REVERT: F 294 VAL cc_start: 0.7427 (t) cc_final: 0.7170 (t) REVERT: F 328 PHE cc_start: 0.8405 (t80) cc_final: 0.8083 (t80) REVERT: F 338 LEU cc_start: 0.8844 (mt) cc_final: 0.8610 (mt) REVERT: F 339 MET cc_start: 0.8123 (mtt) cc_final: 0.7608 (mpp) REVERT: F 390 LYS cc_start: 0.9435 (mttt) cc_final: 0.9194 (mttm) REVERT: P 55 MET cc_start: 0.7705 (tpt) cc_final: 0.6058 (mpp) REVERT: P 78 LYS cc_start: 0.8775 (mttt) cc_final: 0.8513 (mttp) REVERT: P 186 CYS cc_start: 0.9495 (m) cc_final: 0.9038 (p) REVERT: P 202 GLU cc_start: 0.8956 (pm20) cc_final: 0.8746 (pm20) REVERT: P 225 TRP cc_start: 0.9045 (t-100) cc_final: 0.8623 (t-100) REVERT: P 240 LYS cc_start: 0.7632 (mmmm) cc_final: 0.7264 (tttt) REVERT: P 272 PHE cc_start: 0.8012 (p90) cc_final: 0.7703 (p90) REVERT: P 274 GLU cc_start: 0.6479 (mp0) cc_final: 0.5947 (mp0) REVERT: Q 130 ILE cc_start: 0.9203 (mt) cc_final: 0.8811 (mt) REVERT: Z 24 PHE cc_start: 0.7968 (m-80) cc_final: 0.7424 (m-80) REVERT: Z 33 TYR cc_start: 0.8684 (t80) cc_final: 0.8133 (t80) REVERT: Z 70 GLU cc_start: 0.9283 (mp0) cc_final: 0.8713 (mp0) REVERT: Z 75 TRP cc_start: 0.8599 (m-10) cc_final: 0.8366 (m-10) REVERT: Z 86 VAL cc_start: 0.7929 (t) cc_final: 0.7626 (m) REVERT: Z 153 LEU cc_start: 0.6406 (mt) cc_final: 0.5940 (pt) REVERT: Z 196 MET cc_start: 0.6737 (tmm) cc_final: 0.6167 (tmm) outliers start: 1 outliers final: 1 residues processed: 630 average time/residue: 0.1391 time to fit residues: 140.1835 Evaluate side-chains 494 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 493 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 210 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 112 optimal weight: 0.0470 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 396 HIS ** D 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.114162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.087661 restraints weight = 61123.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090620 restraints weight = 37509.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092661 restraints weight = 26296.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094092 restraints weight = 20255.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095117 restraints weight = 16768.340| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20823 Z= 0.207 Angle : 0.776 12.618 28246 Z= 0.396 Chirality : 0.050 0.281 3359 Planarity : 0.005 0.090 3526 Dihedral : 11.495 176.766 2944 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.37 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.17 % Twisted General : 0.16 % 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 (0.17), residues: 2541 helix: -0.14 (0.15), residues: 1153 sheet: -1.20 (0.28), residues: 351 loop : -1.84 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 132 TYR 0.038 0.002 TYR A 331 PHE 0.032 0.002 PHE B 218 TRP 0.021 0.002 TRP A 221 HIS 0.015 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (20809) covalent geometry : angle 0.77637 / 0.40 (28244) SS BOND : bond 0.00311 / 0.16 ( 1) SS BOND : angle 0.08925 / 0.06 ( 2) hydrogen bonds : bond 0.03983 / 2.66 ( 961) hydrogen bonds : angle 5.51111 / 3.88 ( 2766) Misc. bond : bond 0.00233 / 0.17 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3942.76 seconds wall clock time: 69 minutes 1.46 seconds (4141.46 seconds total)