Starting phenix.real_space_refine on Thu Mar 5 10:09:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wj6_21690/03_2026/6wj6_21690_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wj6_21690/03_2026/6wj6_21690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wj6_21690/03_2026/6wj6_21690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wj6_21690/03_2026/6wj6_21690.map" model { file = "/net/cci-nas-00/data/ceres_data/6wj6_21690/03_2026/6wj6_21690_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wj6_21690/03_2026/6wj6_21690_neut.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 8 Type Number sf(0) Gaussians Fe 2 7.16 5 P 4 5.49 5 Mg 35 5.21 5 S 69 5.16 5 Cl 1 4.86 5 C 13000 2.51 5 N 2603 2.21 5 O 3170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18884 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3751 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 26, 'TRANS': 451} Chain: "C" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3259 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 392} Chain breaks: 2 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2734 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 603 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "F" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "H" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "I" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 276 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "K" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 278 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain: "L" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 252 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "M" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "X" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 262 Classifications: {'peptide': 35} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 392 Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1, 'PHO': 1, 'PL9': 1, 'SQD': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1301 Unusual residues: {'BCR': 3, 'CLA': 16, 'LMG': 1, 'LMT': 2, 'SQD': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 1102 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 1, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 554 Unusual residues: {' CL': 1, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 3, 'LMG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'SQD': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCR': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.02, per 1000 atoms: 0.21 Number of scatterers: 18884 At special positions: 0 Unit cell: (108.675, 133.481, 107.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 2 26.01 Cl 1 17.00 S 69 16.00 P 4 15.00 Mg 35 11.99 O 3170 8.00 N 2603 7.00 C 13000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 581.2 milliseconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 8 sheets defined 66.7% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.624A pdb=" N TRP A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 55 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.833A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.884A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.588A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 249 through 259 removed outlier: 3.657A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.923A pdb=" N VAL A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 13 removed outlier: 3.689A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.879A pdb=" N GLY B 59 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.008A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 219 removed outlier: 4.000A pdb=" N VAL B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 234 through 259 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.934A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.643A pdb=" N GLU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.524A pdb=" N TRP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.667A pdb=" N ASP B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.803A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 removed outlier: 6.015A pdb=" N ASN C 26 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 removed outlier: 3.773A pdb=" N THR C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.696A pdb=" N GLN C 71 " --> pdb=" O MET C 68 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 72 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.724A pdb=" N LEU C 82 " --> pdb=" O HIS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 removed outlier: 3.523A pdb=" N PHE C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 169 removed outlier: 3.614A pdb=" N LEU C 154 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 216 through 240 removed outlier: 3.699A pdb=" N ILE C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.672A pdb=" N TRP C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 292 through 309 removed outlier: 3.826A pdb=" N SER C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 removed outlier: 3.995A pdb=" N ARG C 344 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP C 346 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 372 through 382 Processing helix chain 'C' and resid 383 through 386 Processing helix chain 'C' and resid 408 through 441 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.957A pdb=" N PHE C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET C 456 " --> pdb=" O PRO C 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 456' Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 33 through 54 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 109 through 137 removed outlier: 3.512A pdb=" N PHE D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.403A pdb=" N GLY D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 175 through 188 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 221 Processing helix chain 'D' and resid 230 through 234 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 3.780A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 17 through 23 removed outlier: 4.041A pdb=" N ILE E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS E 23 " --> pdb=" O TYR E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 removed outlier: 3.520A pdb=" N GLY E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 48 removed outlier: 3.842A pdb=" N ASP E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'F' and resid 16 through 40 removed outlier: 3.840A pdb=" N LEU F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Proline residue: F 28 - end of helix Processing helix chain 'H' and resid 5 through 11 Processing helix chain 'H' and resid 12 through 16 removed outlier: 3.990A pdb=" N SER H 16 " --> pdb=" O PRO H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 50 Processing helix chain 'I' and resid 3 through 25 removed outlier: 3.688A pdb=" N SER I 17 " --> pdb=" O GLY I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 30 Processing helix chain 'K' and resid 11 through 15 removed outlier: 3.510A pdb=" N GLN K 15 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 22 Processing helix chain 'K' and resid 23 through 25 No H-bonds generated for 'chain 'K' and resid 23 through 25' Processing helix chain 'K' and resid 26 through 31 Processing helix chain 'K' and resid 31 through 43 removed outlier: 3.908A pdb=" N PHE K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA K 40 " --> pdb=" O PHE K 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 39 removed outlier: 4.747A pdb=" N SER L 35 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 28 removed outlier: 3.845A pdb=" N VAL M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) Proline residue: M 18 - end of helix Processing helix chain 'T' and resid 3 through 23 Processing helix chain 'X' and resid 2 through 16 Processing helix chain 'X' and resid 23 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA2, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.622A pdb=" N ASP B 431 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.014A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 356 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 172 through 174 Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 330 Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.548A pdb=" N GLY C 361 " --> pdb=" O GLY C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 77 through 78 863 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 7306 1.39 - 1.60: 11874 1.60 - 1.81: 150 1.81 - 2.03: 35 2.03 - 2.24: 109 Bond restraints: 19474 Sorted by residual: bond pdb=" C10 BCR C 519 " pdb=" C11 BCR C 519 " ideal model delta sigma weight residual 1.436 1.172 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C10 BCR X 102 " pdb=" C11 BCR X 102 " ideal model delta sigma weight residual 1.436 1.175 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C10 BCR B 618 " pdb=" C11 BCR B 618 " ideal model delta sigma weight residual 1.436 1.177 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C10 BCR B 617 " pdb=" C11 BCR B 617 " ideal model delta sigma weight residual 1.436 1.178 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C10 BCR C 516 " pdb=" C11 BCR C 516 " ideal model delta sigma weight residual 1.436 1.179 0.257 2.00e-02 2.50e+03 1.65e+02 ... (remaining 19469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.46: 26716 11.46 - 22.91: 99 22.91 - 34.37: 37 34.37 - 45.83: 18 45.83 - 57.28: 9 Bond angle restraints: 26879 Sorted by residual: angle pdb=" C10 BCR X 102 " pdb=" C11 BCR X 102 " pdb=" C12 BCR X 102 " ideal model delta sigma weight residual 122.66 179.94 -57.28 3.00e+00 1.11e-01 3.65e+02 angle pdb=" C10 BCR D 407 " pdb=" C11 BCR D 407 " pdb=" C12 BCR D 407 " ideal model delta sigma weight residual 122.66 177.86 -55.20 3.00e+00 1.11e-01 3.39e+02 angle pdb=" C10 BCR B 618 " pdb=" C11 BCR B 618 " pdb=" C12 BCR B 618 " ideal model delta sigma weight residual 122.66 177.61 -54.95 3.00e+00 1.11e-01 3.35e+02 angle pdb=" C10 BCR B 619 " pdb=" C11 BCR B 619 " pdb=" C12 BCR B 619 " ideal model delta sigma weight residual 122.66 177.34 -54.68 3.00e+00 1.11e-01 3.32e+02 angle pdb=" C10 BCR C 516 " pdb=" C11 BCR C 516 " pdb=" C12 BCR C 516 " ideal model delta sigma weight residual 122.66 177.23 -54.57 3.00e+00 1.11e-01 3.31e+02 ... (remaining 26874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.82: 9376 25.82 - 51.64: 732 51.64 - 77.45: 163 77.45 - 103.27: 19 103.27 - 129.09: 12 Dihedral angle restraints: 10302 sinusoidal: 4953 harmonic: 5349 Sorted by residual: dihedral pdb=" CA PHE A 260 " pdb=" C PHE A 260 " pdb=" N GLN A 261 " pdb=" CA GLN A 261 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA ASP C 365 " pdb=" C ASP C 365 " pdb=" N LYS C 366 " pdb=" CA LYS C 366 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY C 209 " pdb=" C GLY C 209 " pdb=" N TRP C 210 " pdb=" CA TRP C 210 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 10299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2464 0.157 - 0.314: 51 0.314 - 0.471: 10 0.471 - 0.628: 19 0.628 - 0.785: 9 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C3A CLA B 604 " pdb=" C2A CLA B 604 " pdb=" C4A CLA B 604 " pdb=" CMA CLA B 604 " both_signs ideal model delta sigma weight residual False -2.76 -1.98 -0.79 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C3A CLA C 512 " pdb=" C2A CLA C 512 " pdb=" C4A CLA C 512 " pdb=" CMA CLA C 512 " both_signs ideal model delta sigma weight residual False -2.76 -2.04 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C3A CLA C 504 " pdb=" C2A CLA C 504 " pdb=" C4A CLA C 504 " pdb=" CMA CLA C 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.04 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2550 not shown) Planarity restraints: 3320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " 0.117 2.00e-02 2.50e+03 1.31e-01 1.37e+03 pdb=" ND PHO A 404 " 0.055 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " -0.015 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " 0.063 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " 0.010 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " -0.014 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " -0.180 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " -0.114 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " 0.065 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " -0.042 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " 0.340 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " -0.150 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " 0.053 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " -0.061 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " 0.238 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " -0.001 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " -0.017 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " -0.025 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " -0.294 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " 0.098 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " -0.076 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " -0.146 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " -0.060 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " 0.155 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " 0.028 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " -0.049 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " -0.202 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " 0.132 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " -0.051 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " 0.234 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " -0.042 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 403 " -0.048 2.00e-02 2.50e+03 1.27e-01 1.28e+03 pdb=" ND PHO D 403 " 0.189 2.00e-02 2.50e+03 pdb=" C1A PHO D 403 " -0.045 2.00e-02 2.50e+03 pdb=" C1B PHO D 403 " -0.022 2.00e-02 2.50e+03 pdb=" C1C PHO D 403 " -0.001 2.00e-02 2.50e+03 pdb=" C1D PHO D 403 " 0.075 2.00e-02 2.50e+03 pdb=" C2A PHO D 403 " 0.089 2.00e-02 2.50e+03 pdb=" C2B PHO D 403 " 0.115 2.00e-02 2.50e+03 pdb=" C2C PHO D 403 " -0.076 2.00e-02 2.50e+03 pdb=" C2D PHO D 403 " 0.075 2.00e-02 2.50e+03 pdb=" C3A PHO D 403 " -0.311 2.00e-02 2.50e+03 pdb=" C3B PHO D 403 " 0.149 2.00e-02 2.50e+03 pdb=" C3C PHO D 403 " -0.102 2.00e-02 2.50e+03 pdb=" C3D PHO D 403 " 0.073 2.00e-02 2.50e+03 pdb=" C4A PHO D 403 " -0.203 2.00e-02 2.50e+03 pdb=" C4B PHO D 403 " 0.041 2.00e-02 2.50e+03 pdb=" C4C PHO D 403 " -0.030 2.00e-02 2.50e+03 pdb=" C4D PHO D 403 " 0.078 2.00e-02 2.50e+03 pdb=" CAB PHO D 403 " 0.240 2.00e-02 2.50e+03 pdb=" CAC PHO D 403 " -0.186 2.00e-02 2.50e+03 pdb=" CAD PHO D 403 " 0.069 2.00e-02 2.50e+03 pdb=" CBD PHO D 403 " -0.110 2.00e-02 2.50e+03 pdb=" CHA PHO D 403 " -0.024 2.00e-02 2.50e+03 pdb=" CHB PHO D 403 " -0.109 2.00e-02 2.50e+03 pdb=" CHC PHO D 403 " 0.005 2.00e-02 2.50e+03 pdb=" CHD PHO D 403 " -0.028 2.00e-02 2.50e+03 pdb=" CMB PHO D 403 " 0.163 2.00e-02 2.50e+03 pdb=" CMC PHO D 403 " -0.132 2.00e-02 2.50e+03 pdb=" CMD PHO D 403 " 0.067 2.00e-02 2.50e+03 pdb=" NA PHO D 403 " -0.214 2.00e-02 2.50e+03 pdb=" NC PHO D 403 " 0.033 2.00e-02 2.50e+03 pdb=" OBD PHO D 403 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR C 519 " -0.290 2.00e-02 2.50e+03 1.68e-01 3.51e+02 pdb=" C11 BCR C 519 " 0.200 2.00e-02 2.50e+03 pdb=" C34 BCR C 519 " 0.064 2.00e-02 2.50e+03 pdb=" C8 BCR C 519 " 0.089 2.00e-02 2.50e+03 pdb=" C9 BCR C 519 " -0.062 2.00e-02 2.50e+03 ... (remaining 3317 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 351 2.65 - 3.21: 16288 3.21 - 3.77: 31536 3.77 - 4.34: 48433 4.34 - 4.90: 74435 Nonbonded interactions: 171043 Sorted by model distance: nonbonded pdb=" OE1 GLN C 298 " pdb=" OG1 THR C 342 " model vdw 2.082 3.040 nonbonded pdb=" O TYR C 258 " pdb=" O HOH C 601 " model vdw 2.143 3.040 nonbonded pdb=" O LEU M 25 " pdb=" OG1 THR M 29 " model vdw 2.153 3.040 nonbonded pdb=" O ASN B 191 " pdb=" O HOH B 701 " model vdw 2.159 3.040 nonbonded pdb=" O HOH A 502 " pdb=" O HOH A 552 " model vdw 2.175 3.040 ... (remaining 171038 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 : 0.036 0.924 19507 Z= 2.461 Angle : 2.549 57.283 26879 Z= 0.881 Chirality : 0.086 0.785 2553 Planarity : 0.012 0.168 3320 Dihedral : 18.877 129.089 6888 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.58 (0.16), residues: 1866 helix: -2.86 (0.11), residues: 1087 sheet: -2.78 (0.65), residues: 49 loop : -1.20 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 294 TYR 0.016 0.002 TYR H 49 PHE 0.030 0.002 PHE B 246 TRP 0.018 0.002 TRP A 131 HIS 0.006 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.02490 (19474) covalent geometry : angle 2.54891 (26879) hydrogen bonds : bond 0.25337 ( 863) hydrogen bonds : angle 9.51446 ( 2427) Misc. bond : bond 0.64426 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.7123 (t0) cc_final: 0.6740 (t0) REVERT: A 86 SER cc_start: 0.8798 (t) cc_final: 0.8577 (t) REVERT: A 87 ASN cc_start: 0.8292 (t0) cc_final: 0.8076 (t0) REVERT: A 214 MET cc_start: 0.7978 (tpt) cc_final: 0.7757 (mmm) REVERT: A 293 MET cc_start: 0.7648 (mtm) cc_final: 0.7440 (mtp) REVERT: B 231 MET cc_start: 0.9135 (mtt) cc_final: 0.8777 (mtt) REVERT: B 347 LYS cc_start: 0.8174 (mttm) cc_final: 0.7946 (mttm) REVERT: B 349 LYS cc_start: 0.7357 (pttm) cc_final: 0.6802 (pttp) REVERT: B 359 MET cc_start: 0.8785 (ttm) cc_final: 0.8579 (ttp) REVERT: B 422 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7755 (mtt-85) REVERT: C 65 GLU cc_start: 0.7149 (pm20) cc_final: 0.6891 (pm20) REVERT: C 91 GLU cc_start: 0.7722 (mp0) cc_final: 0.7328 (mp0) REVERT: C 169 PHE cc_start: 0.6989 (m-80) cc_final: 0.6761 (m-80) REVERT: D 317 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8321 (mtpt) REVERT: D 343 GLU cc_start: 0.6856 (tp30) cc_final: 0.6583 (tp30) REVERT: D 348 ARG cc_start: 0.7605 (ptp90) cc_final: 0.6921 (ptp-110) REVERT: F 40 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8611 (mm-40) REVERT: H 9 ASP cc_start: 0.7929 (m-30) cc_final: 0.7499 (m-30) REVERT: I 30 ARG cc_start: 0.7207 (mtt-85) cc_final: 0.6747 (mmt90) REVERT: L 23 LEU cc_start: 0.8320 (mt) cc_final: 0.8090 (OUTLIER) REVERT: X 32 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7457 (mm110) outliers start: 0 outliers final: 2 residues processed: 269 average time/residue: 0.6608 time to fit residues: 198.4143 Evaluate side-chains 210 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS A 332 HIS B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN B 331 ASN B 413 ASN B 438 ASN C 142 ASN C 300 GLN C 309 GLN C 385 HIS D 142 ASN D 263 ASN E 67 GLN H 3 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102366 restraints weight = 22011.125| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.45 r_work: 0.2984 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 19507 Z= 0.172 Angle : 0.676 9.810 26879 Z= 0.313 Chirality : 0.045 0.191 2553 Planarity : 0.006 0.048 3320 Dihedral : 19.511 126.279 3655 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 1.75 % Allowed : 7.58 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 1866 helix: -0.25 (0.14), residues: 1112 sheet: -2.46 (0.65), residues: 49 loop : -0.64 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 122 TYR 0.013 0.002 TYR B 172 PHE 0.030 0.002 PHE B 246 TRP 0.019 0.002 TRP A 131 HIS 0.007 0.002 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00375 (19474) covalent geometry : angle 0.67578 (26879) hydrogen bonds : bond 0.05414 ( 863) hydrogen bonds : angle 5.18204 ( 2427) Misc. bond : bond 0.03930 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.618 Fit side-chains REVERT: A 59 ASP cc_start: 0.7951 (t0) cc_final: 0.7306 (t0) REVERT: A 87 ASN cc_start: 0.8439 (t0) cc_final: 0.8123 (t0) REVERT: A 322 ASN cc_start: 0.8611 (t0) cc_final: 0.8316 (t0) REVERT: B 22 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8836 (m) REVERT: B 130 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6987 (mm-30) REVERT: B 231 MET cc_start: 0.9338 (mtt) cc_final: 0.9020 (mtt) REVERT: B 286 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7696 (ttm-80) REVERT: B 347 LYS cc_start: 0.8219 (mttm) cc_final: 0.7911 (mttm) REVERT: B 349 LYS cc_start: 0.7705 (pttm) cc_final: 0.7067 (pttp) REVERT: B 350 GLU cc_start: 0.7217 (mp0) cc_final: 0.6745 (mp0) REVERT: B 387 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: C 125 GLU cc_start: 0.8100 (tt0) cc_final: 0.7867 (mt-10) REVERT: C 169 PHE cc_start: 0.7068 (m-80) cc_final: 0.6618 (m-80) REVERT: C 229 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8294 (mm) REVERT: C 366 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7347 (mttp) REVERT: C 372 GLN cc_start: 0.7424 (mm-40) cc_final: 0.6860 (mm110) REVERT: D 348 ARG cc_start: 0.7609 (ptp90) cc_final: 0.7095 (ptp-110) REVERT: E 39 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8527 (p) REVERT: H 4 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7813 (mtp180) REVERT: H 9 ASP cc_start: 0.8096 (m-30) cc_final: 0.7755 (m-30) REVERT: H 12 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6990 (tpm170) REVERT: H 31 MET cc_start: 0.8863 (ttp) cc_final: 0.8538 (ttp) REVERT: I 30 ARG cc_start: 0.7131 (mtt-85) cc_final: 0.6502 (mmt90) REVERT: L 23 LEU cc_start: 0.8058 (mt) cc_final: 0.7781 (mp) outliers start: 27 outliers final: 10 residues processed: 227 average time/residue: 0.6502 time to fit residues: 165.2172 Evaluate side-chains 217 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 87 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 413 ASN B 438 ASN C 375 GLN D 142 ASN D 263 ASN E 67 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101888 restraints weight = 22117.780| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.46 r_work: 0.2968 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 19507 Z= 0.189 Angle : 0.654 8.861 26879 Z= 0.302 Chirality : 0.046 0.215 2553 Planarity : 0.005 0.049 3320 Dihedral : 18.879 125.118 3653 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.64 % Rotamer: Outliers : 2.14 % Allowed : 9.27 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1866 helix: 0.71 (0.15), residues: 1113 sheet: -2.09 (0.66), residues: 49 loop : -0.41 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 60 TYR 0.014 0.002 TYR B 172 PHE 0.028 0.002 PHE B 246 TRP 0.020 0.002 TRP A 131 HIS 0.007 0.002 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00431 (19474) covalent geometry : angle 0.65385 (26879) hydrogen bonds : bond 0.05165 ( 863) hydrogen bonds : angle 4.82990 ( 2427) Misc. bond : bond 0.03535 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.595 Fit side-chains REVERT: A 59 ASP cc_start: 0.7901 (t0) cc_final: 0.7548 (t0) REVERT: A 87 ASN cc_start: 0.8416 (t0) cc_final: 0.8116 (t0) REVERT: A 107 TYR cc_start: 0.9398 (t80) cc_final: 0.9117 (t80) REVERT: A 322 ASN cc_start: 0.8694 (t0) cc_final: 0.8405 (t0) REVERT: B 130 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 231 MET cc_start: 0.9336 (mtt) cc_final: 0.9041 (mtt) REVERT: B 286 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7694 (ttm-80) REVERT: B 347 LYS cc_start: 0.8171 (mttm) cc_final: 0.7868 (mttm) REVERT: B 349 LYS cc_start: 0.7909 (pttm) cc_final: 0.7424 (pttp) REVERT: B 350 GLU cc_start: 0.7105 (mp0) cc_final: 0.6693 (mp0) REVERT: B 370 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8939 (mtm) REVERT: B 387 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6678 (mm-30) REVERT: C 65 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: C 169 PHE cc_start: 0.7038 (m-80) cc_final: 0.6613 (m-80) REVERT: C 366 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7433 (mttp) REVERT: C 368 ARG cc_start: 0.6756 (mmt-90) cc_final: 0.5964 (mmp80) REVERT: C 377 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7778 (mtp180) REVERT: C 381 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7624 (tt0) REVERT: D 348 ARG cc_start: 0.7663 (ptp90) cc_final: 0.7130 (ptp-110) REVERT: E 20 TRP cc_start: 0.6640 (OUTLIER) cc_final: 0.6339 (m-90) REVERT: F 39 MET cc_start: 0.9157 (mtt) cc_final: 0.8683 (mtm) REVERT: H 4 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7784 (mtp180) REVERT: H 9 ASP cc_start: 0.8241 (m-30) cc_final: 0.7874 (m-30) REVERT: H 31 MET cc_start: 0.8804 (ttp) cc_final: 0.8460 (ttp) REVERT: I 30 ARG cc_start: 0.7160 (mtt-85) cc_final: 0.6499 (mmt90) REVERT: L 23 LEU cc_start: 0.8050 (mt) cc_final: 0.7776 (mp) REVERT: M 6 LEU cc_start: 0.8603 (mp) cc_final: 0.8284 (mm) outliers start: 33 outliers final: 18 residues processed: 227 average time/residue: 0.6308 time to fit residues: 160.7118 Evaluate side-chains 223 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 413 ASN B 438 ASN C 298 GLN D 336 HIS E 67 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101920 restraints weight = 22209.911| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.46 r_work: 0.2998 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 19507 Z= 0.161 Angle : 0.600 8.662 26879 Z= 0.279 Chirality : 0.044 0.200 2553 Planarity : 0.005 0.049 3320 Dihedral : 18.263 124.904 3653 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.20 % Favored : 97.75 % Rotamer: Outliers : 1.88 % Allowed : 10.56 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1866 helix: 1.11 (0.16), residues: 1112 sheet: -1.81 (0.67), residues: 49 loop : -0.28 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 122 TYR 0.013 0.002 TYR B 172 PHE 0.028 0.002 PHE B 246 TRP 0.019 0.002 TRP A 131 HIS 0.007 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00368 (19474) covalent geometry : angle 0.60047 (26879) hydrogen bonds : bond 0.04616 ( 863) hydrogen bonds : angle 4.64513 ( 2427) Misc. bond : bond 0.02973 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.7899 (t0) cc_final: 0.7528 (t0) REVERT: A 87 ASN cc_start: 0.8399 (t0) cc_final: 0.8155 (t0) REVERT: A 107 TYR cc_start: 0.9394 (t80) cc_final: 0.9122 (t80) REVERT: A 322 ASN cc_start: 0.8699 (t0) cc_final: 0.8403 (t0) REVERT: B 130 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6912 (mm-30) REVERT: B 231 MET cc_start: 0.9322 (mtt) cc_final: 0.9018 (mtt) REVERT: B 286 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7680 (ttm-80) REVERT: B 347 LYS cc_start: 0.8128 (mttm) cc_final: 0.7842 (mttm) REVERT: B 349 LYS cc_start: 0.7839 (pttm) cc_final: 0.7208 (pttp) REVERT: B 350 GLU cc_start: 0.7175 (mp0) cc_final: 0.6743 (mp0) REVERT: B 387 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: C 65 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: C 169 PHE cc_start: 0.7032 (m-80) cc_final: 0.6622 (m-80) REVERT: C 366 LYS cc_start: 0.7712 (mtpt) cc_final: 0.7374 (mttp) REVERT: C 368 ARG cc_start: 0.6647 (mmt-90) cc_final: 0.5858 (mmp80) REVERT: C 372 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6889 (mm110) REVERT: C 377 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7819 (mtp180) REVERT: C 381 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7628 (tt0) REVERT: D 299 VAL cc_start: 0.8917 (m) cc_final: 0.8704 (t) REVERT: D 348 ARG cc_start: 0.7669 (ptp90) cc_final: 0.7414 (ptt-90) REVERT: E 20 TRP cc_start: 0.6465 (OUTLIER) cc_final: 0.6225 (m-90) REVERT: E 39 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8543 (p) REVERT: F 39 MET cc_start: 0.9179 (mtt) cc_final: 0.8644 (mtm) REVERT: H 4 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7800 (mtp180) REVERT: H 9 ASP cc_start: 0.8127 (m-30) cc_final: 0.7736 (m-30) REVERT: H 31 MET cc_start: 0.8815 (ttp) cc_final: 0.8480 (ttp) REVERT: I 30 ARG cc_start: 0.7148 (mtt-85) cc_final: 0.6543 (mmt90) REVERT: K 22 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: L 23 LEU cc_start: 0.8048 (mt) cc_final: 0.7783 (mp) REVERT: M 6 LEU cc_start: 0.8627 (mp) cc_final: 0.8300 (mm) outliers start: 29 outliers final: 13 residues processed: 224 average time/residue: 0.6594 time to fit residues: 164.7632 Evaluate side-chains 217 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 114 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 438 ASN C 375 GLN D 263 ASN D 336 HIS H 3 GLN M 5 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103719 restraints weight = 22003.974| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.45 r_work: 0.3015 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 19507 Z= 0.133 Angle : 0.562 8.638 26879 Z= 0.261 Chirality : 0.042 0.189 2553 Planarity : 0.004 0.049 3320 Dihedral : 17.698 123.857 3653 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 2.27 % Allowed : 10.56 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1866 helix: 1.44 (0.16), residues: 1108 sheet: -1.60 (0.69), residues: 49 loop : -0.08 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 122 TYR 0.011 0.001 TYR B 172 PHE 0.027 0.001 PHE B 246 TRP 0.017 0.001 TRP A 131 HIS 0.006 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00297 (19474) covalent geometry : angle 0.56242 (26879) hydrogen bonds : bond 0.04273 ( 863) hydrogen bonds : angle 4.46872 ( 2427) Misc. bond : bond 0.02782 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.7888 (t0) cc_final: 0.7517 (t0) REVERT: A 107 TYR cc_start: 0.9395 (t80) cc_final: 0.9125 (t80) REVERT: A 322 ASN cc_start: 0.8705 (t0) cc_final: 0.8429 (t0) REVERT: B 130 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6885 (mm-30) REVERT: B 231 MET cc_start: 0.9285 (mtt) cc_final: 0.8998 (mtt) REVERT: B 286 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7668 (ttm-80) REVERT: B 347 LYS cc_start: 0.8091 (mttm) cc_final: 0.7801 (mttm) REVERT: B 349 LYS cc_start: 0.7850 (pttm) cc_final: 0.7225 (pttp) REVERT: B 350 GLU cc_start: 0.7164 (mp0) cc_final: 0.6722 (mp0) REVERT: B 359 MET cc_start: 0.9219 (ttm) cc_final: 0.8878 (ttp) REVERT: B 387 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: C 65 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: C 169 PHE cc_start: 0.7029 (m-80) cc_final: 0.6615 (m-80) REVERT: C 233 SER cc_start: 0.8632 (m) cc_final: 0.8412 (p) REVERT: C 366 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7343 (mttp) REVERT: C 372 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7053 (mm110) REVERT: C 381 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7605 (tt0) REVERT: D 16 ASP cc_start: 0.7958 (m-30) cc_final: 0.7640 (m-30) REVERT: D 348 ARG cc_start: 0.7643 (ptp90) cc_final: 0.7349 (ptt-90) REVERT: E 20 TRP cc_start: 0.6412 (OUTLIER) cc_final: 0.6177 (m-90) REVERT: E 39 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8543 (p) REVERT: E 62 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7470 (mp0) REVERT: F 39 MET cc_start: 0.9173 (mtt) cc_final: 0.8641 (mtm) REVERT: H 4 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7897 (mtp180) REVERT: H 9 ASP cc_start: 0.8149 (m-30) cc_final: 0.7763 (m-30) REVERT: H 31 MET cc_start: 0.8801 (ttp) cc_final: 0.8479 (ttp) REVERT: I 30 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.6770 (mmt90) REVERT: K 22 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: L 23 LEU cc_start: 0.8060 (mt) cc_final: 0.7797 (mp) REVERT: M 6 LEU cc_start: 0.8640 (mp) cc_final: 0.8322 (mm) REVERT: M 8 PHE cc_start: 0.8468 (t80) cc_final: 0.8230 (t80) REVERT: T 16 VAL cc_start: 0.7589 (t) cc_final: 0.6898 (p) outliers start: 35 outliers final: 18 residues processed: 228 average time/residue: 0.6351 time to fit residues: 162.0838 Evaluate side-chains 230 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 159 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 438 ASN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 336 HIS H 3 GLN M 5 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101334 restraints weight = 22040.050| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.39 r_work: 0.2981 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.224 19507 Z= 0.244 Angle : 0.676 8.932 26879 Z= 0.312 Chirality : 0.048 0.228 2553 Planarity : 0.005 0.051 3320 Dihedral : 18.157 126.862 3653 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 2.53 % Allowed : 11.60 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1866 helix: 1.22 (0.16), residues: 1114 sheet: -1.41 (0.71), residues: 47 loop : -0.16 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 60 TYR 0.017 0.002 TYR B 172 PHE 0.029 0.002 PHE B 246 TRP 0.021 0.002 TRP A 131 HIS 0.010 0.002 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00568 (19474) covalent geometry : angle 0.67589 (26879) hydrogen bonds : bond 0.05219 ( 863) hydrogen bonds : angle 4.72789 ( 2427) Misc. bond : bond 0.04019 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.7841 (t0) cc_final: 0.7477 (t0) REVERT: A 107 TYR cc_start: 0.9392 (t80) cc_final: 0.9130 (t80) REVERT: A 322 ASN cc_start: 0.8680 (t0) cc_final: 0.8397 (t0) REVERT: B 130 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6927 (mm-30) REVERT: B 149 LEU cc_start: 0.8930 (tp) cc_final: 0.8726 (tp) REVERT: B 231 MET cc_start: 0.9359 (mtt) cc_final: 0.9043 (mtt) REVERT: B 286 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7663 (ttm-80) REVERT: B 349 LYS cc_start: 0.7915 (pttm) cc_final: 0.7345 (pttp) REVERT: B 350 GLU cc_start: 0.7238 (mp0) cc_final: 0.6871 (mp0) REVERT: B 359 MET cc_start: 0.9206 (ttm) cc_final: 0.8955 (ttp) REVERT: B 387 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: C 169 PHE cc_start: 0.6940 (m-80) cc_final: 0.6605 (m-80) REVERT: C 366 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7454 (mttp) REVERT: C 368 ARG cc_start: 0.7029 (mmt180) cc_final: 0.6782 (mmt180) REVERT: C 372 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6979 (mm110) REVERT: D 16 ASP cc_start: 0.8130 (m-30) cc_final: 0.7712 (m-30) REVERT: E 20 TRP cc_start: 0.6363 (OUTLIER) cc_final: 0.6126 (m-90) REVERT: E 68 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: F 40 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8613 (mm-40) REVERT: H 31 MET cc_start: 0.8809 (ttp) cc_final: 0.8482 (ttp) REVERT: I 30 ARG cc_start: 0.7369 (mtt-85) cc_final: 0.6681 (mmt90) REVERT: L 23 LEU cc_start: 0.8106 (mt) cc_final: 0.7858 (mp) REVERT: M 6 LEU cc_start: 0.8661 (mp) cc_final: 0.8352 (mm) REVERT: T 16 VAL cc_start: 0.7740 (t) cc_final: 0.7040 (p) outliers start: 39 outliers final: 24 residues processed: 231 average time/residue: 0.6704 time to fit residues: 172.5092 Evaluate side-chains 228 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN C 375 GLN E 67 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104486 restraints weight = 22136.447| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.38 r_work: 0.3004 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 19507 Z= 0.122 Angle : 0.562 9.016 26879 Z= 0.261 Chirality : 0.042 0.196 2553 Planarity : 0.004 0.051 3320 Dihedral : 17.451 123.675 3653 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.94 % Allowed : 11.99 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1866 helix: 1.54 (0.16), residues: 1115 sheet: -1.52 (0.71), residues: 49 loop : -0.04 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 122 TYR 0.011 0.001 TYR B 172 PHE 0.028 0.001 PHE B 246 TRP 0.018 0.001 TRP A 131 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00266 (19474) covalent geometry : angle 0.56164 (26879) hydrogen bonds : bond 0.04199 ( 863) hydrogen bonds : angle 4.46220 ( 2427) Misc. bond : bond 0.02736 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.522 Fit side-chains REVERT: A 59 ASP cc_start: 0.7768 (t0) cc_final: 0.7438 (t0) REVERT: A 107 TYR cc_start: 0.9399 (t80) cc_final: 0.9136 (t80) REVERT: A 172 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8925 (ttp) REVERT: A 322 ASN cc_start: 0.8779 (t0) cc_final: 0.8525 (t0) REVERT: B 22 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8688 (m) REVERT: B 231 MET cc_start: 0.9309 (mtt) cc_final: 0.9014 (mtt) REVERT: B 286 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7697 (ttm-80) REVERT: B 347 LYS cc_start: 0.8020 (mttm) cc_final: 0.7789 (mttm) REVERT: B 349 LYS cc_start: 0.7894 (pttm) cc_final: 0.7356 (pttp) REVERT: B 350 GLU cc_start: 0.7177 (mp0) cc_final: 0.6782 (mp0) REVERT: B 359 MET cc_start: 0.9214 (ttm) cc_final: 0.8923 (ttp) REVERT: B 387 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6724 (mm-30) REVERT: C 169 PHE cc_start: 0.6952 (m-80) cc_final: 0.6547 (m-80) REVERT: C 366 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7376 (mttp) REVERT: C 372 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7066 (mm110) REVERT: D 16 ASP cc_start: 0.8071 (m-30) cc_final: 0.7653 (m-30) REVERT: D 348 ARG cc_start: 0.7868 (ptt-90) cc_final: 0.7622 (ptp90) REVERT: E 20 TRP cc_start: 0.6214 (OUTLIER) cc_final: 0.5979 (m-90) REVERT: E 62 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7491 (mp0) REVERT: E 68 GLU cc_start: 0.7521 (pt0) cc_final: 0.7160 (pp20) REVERT: F 39 MET cc_start: 0.9180 (mtt) cc_final: 0.8645 (mtm) REVERT: H 9 ASP cc_start: 0.8138 (m-30) cc_final: 0.7818 (m-30) REVERT: H 31 MET cc_start: 0.8792 (ttp) cc_final: 0.8453 (ttp) REVERT: I 30 ARG cc_start: 0.7512 (mtt-85) cc_final: 0.6820 (mmt90) REVERT: K 22 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: L 23 LEU cc_start: 0.8099 (mt) cc_final: 0.7848 (mp) REVERT: M 6 LEU cc_start: 0.8631 (mp) cc_final: 0.8338 (mm) REVERT: M 8 PHE cc_start: 0.8479 (t80) cc_final: 0.8167 (t80) REVERT: T 16 VAL cc_start: 0.7639 (t) cc_final: 0.6963 (p) outliers start: 30 outliers final: 15 residues processed: 221 average time/residue: 0.6347 time to fit residues: 156.8824 Evaluate side-chains 220 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 127 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 152 optimal weight: 0.2980 chunk 179 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 0.0040 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 438 ASN H 3 GLN M 5 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108866 restraints weight = 21933.288| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.37 r_work: 0.3088 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.122 19507 Z= 0.098 Angle : 0.527 8.616 26879 Z= 0.244 Chirality : 0.040 0.180 2553 Planarity : 0.004 0.051 3320 Dihedral : 16.639 121.616 3653 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.10 % Allowed : 13.16 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.20), residues: 1866 helix: 1.87 (0.16), residues: 1106 sheet: -1.44 (0.67), residues: 49 loop : 0.16 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 122 TYR 0.010 0.001 TYR A 147 PHE 0.024 0.001 PHE B 246 TRP 0.018 0.001 TRP A 131 HIS 0.005 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00204 (19474) covalent geometry : angle 0.52674 (26879) hydrogen bonds : bond 0.03652 ( 863) hydrogen bonds : angle 4.22773 ( 2427) Misc. bond : bond 0.02136 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.629 Fit side-chains REVERT: A 59 ASP cc_start: 0.7731 (t0) cc_final: 0.7416 (t0) REVERT: A 107 TYR cc_start: 0.9375 (t80) cc_final: 0.9094 (t80) REVERT: A 322 ASN cc_start: 0.8738 (t0) cc_final: 0.8498 (t0) REVERT: B 22 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8697 (m) REVERT: B 108 PHE cc_start: 0.8532 (t80) cc_final: 0.8217 (t80) REVERT: B 231 MET cc_start: 0.9259 (mtt) cc_final: 0.8971 (mtt) REVERT: B 347 LYS cc_start: 0.7917 (mttm) cc_final: 0.7710 (mttm) REVERT: B 350 GLU cc_start: 0.7188 (mp0) cc_final: 0.6958 (mp0) REVERT: B 359 MET cc_start: 0.9115 (ttm) cc_final: 0.8747 (ttp) REVERT: B 387 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6826 (mm-30) REVERT: C 169 PHE cc_start: 0.6667 (m-80) cc_final: 0.6366 (m-80) REVERT: C 366 LYS cc_start: 0.7628 (mtpt) cc_final: 0.7296 (mttp) REVERT: C 372 GLN cc_start: 0.7300 (mm-40) cc_final: 0.6991 (mm110) REVERT: D 16 ASP cc_start: 0.7916 (m-30) cc_final: 0.7656 (m-30) REVERT: D 271 MET cc_start: 0.8993 (mtp) cc_final: 0.8726 (mtm) REVERT: D 348 ARG cc_start: 0.7899 (ptt-90) cc_final: 0.7236 (ptp-110) REVERT: E 20 TRP cc_start: 0.6181 (OUTLIER) cc_final: 0.5952 (m-90) REVERT: E 62 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7446 (mp0) REVERT: E 68 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7153 (pp20) REVERT: F 39 MET cc_start: 0.9131 (mtt) cc_final: 0.8597 (mtm) REVERT: H 9 ASP cc_start: 0.8139 (m-30) cc_final: 0.7867 (m-30) REVERT: H 31 MET cc_start: 0.8828 (ttp) cc_final: 0.8509 (ttp) REVERT: I 30 ARG cc_start: 0.7439 (mtt-85) cc_final: 0.6705 (mmt90) REVERT: K 22 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: L 23 LEU cc_start: 0.8109 (mt) cc_final: 0.7858 (mp) REVERT: M 6 LEU cc_start: 0.8639 (mp) cc_final: 0.8365 (mm) REVERT: T 16 VAL cc_start: 0.7596 (t) cc_final: 0.6947 (p) outliers start: 17 outliers final: 7 residues processed: 218 average time/residue: 0.6414 time to fit residues: 156.4489 Evaluate side-chains 210 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 4 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 72 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN C 375 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104908 restraints weight = 22107.924| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.45 r_work: 0.3047 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 19507 Z= 0.113 Angle : 0.535 8.573 26879 Z= 0.250 Chirality : 0.041 0.211 2553 Planarity : 0.004 0.051 3320 Dihedral : 16.535 122.936 3653 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.17 % Allowed : 13.42 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1866 helix: 1.91 (0.16), residues: 1106 sheet: -1.09 (0.70), residues: 47 loop : 0.17 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.021 0.001 TYR H 18 PHE 0.027 0.001 PHE B 246 TRP 0.017 0.001 TRP A 131 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00247 (19474) covalent geometry : angle 0.53545 (26879) hydrogen bonds : bond 0.03884 ( 863) hydrogen bonds : angle 4.25261 ( 2427) Misc. bond : bond 0.02648 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.648 Fit side-chains REVERT: A 59 ASP cc_start: 0.7719 (t0) cc_final: 0.7392 (t0) REVERT: A 107 TYR cc_start: 0.9367 (t80) cc_final: 0.9034 (t80) REVERT: A 312 ARG cc_start: 0.7512 (mtm180) cc_final: 0.7259 (mtm180) REVERT: A 322 ASN cc_start: 0.8751 (t0) cc_final: 0.8482 (t0) REVERT: B 22 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8797 (m) REVERT: B 130 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6892 (mm-30) REVERT: B 231 MET cc_start: 0.9302 (mtt) cc_final: 0.9008 (mtt) REVERT: B 347 LYS cc_start: 0.7916 (mttm) cc_final: 0.7704 (mttm) REVERT: B 350 GLU cc_start: 0.7193 (mp0) cc_final: 0.6898 (mp0) REVERT: B 359 MET cc_start: 0.9150 (ttm) cc_final: 0.8796 (ttp) REVERT: B 369 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8479 (mm) REVERT: C 169 PHE cc_start: 0.6687 (m-80) cc_final: 0.6398 (m-80) REVERT: C 366 LYS cc_start: 0.7578 (mtpt) cc_final: 0.7251 (mttp) REVERT: C 372 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7148 (mm110) REVERT: D 16 ASP cc_start: 0.8026 (m-30) cc_final: 0.7727 (m-30) REVERT: D 271 MET cc_start: 0.9012 (mtp) cc_final: 0.8797 (mtm) REVERT: D 348 ARG cc_start: 0.7896 (ptt-90) cc_final: 0.7147 (ptp-110) REVERT: E 62 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7469 (mp0) REVERT: E 68 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7161 (pp20) REVERT: F 39 MET cc_start: 0.9165 (mtt) cc_final: 0.8620 (mtm) REVERT: H 9 ASP cc_start: 0.8133 (m-30) cc_final: 0.7703 (m-30) REVERT: H 31 MET cc_start: 0.8802 (ttp) cc_final: 0.8457 (ttp) REVERT: I 30 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.6751 (mmt90) REVERT: K 22 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: L 23 LEU cc_start: 0.8012 (mt) cc_final: 0.7765 (mp) REVERT: M 6 LEU cc_start: 0.8617 (mp) cc_final: 0.8329 (mm) REVERT: T 16 VAL cc_start: 0.7590 (t) cc_final: 0.6924 (p) outliers start: 18 outliers final: 10 residues processed: 204 average time/residue: 0.6740 time to fit residues: 153.0497 Evaluate side-chains 208 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 105 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 162 optimal weight: 0.0020 chunk 62 optimal weight: 2.9990 chunk 154 optimal weight: 0.4980 chunk 180 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN M 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107647 restraints weight = 21866.807| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.38 r_work: 0.3057 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.136 19507 Z= 0.102 Angle : 0.522 8.812 26879 Z= 0.244 Chirality : 0.041 0.234 2553 Planarity : 0.004 0.051 3320 Dihedral : 16.189 122.518 3653 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.17 % Allowed : 13.61 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.20), residues: 1866 helix: 2.04 (0.16), residues: 1107 sheet: -1.11 (0.86), residues: 32 loop : 0.25 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.010 0.001 TYR B 172 PHE 0.026 0.001 PHE B 246 TRP 0.016 0.001 TRP A 131 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00218 (19474) covalent geometry : angle 0.52206 (26879) hydrogen bonds : bond 0.03727 ( 863) hydrogen bonds : angle 4.18981 ( 2427) Misc. bond : bond 0.02391 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.554 Fit side-chains REVERT: A 59 ASP cc_start: 0.7709 (t0) cc_final: 0.7404 (t0) REVERT: A 107 TYR cc_start: 0.9372 (t80) cc_final: 0.9056 (t80) REVERT: A 322 ASN cc_start: 0.8748 (t0) cc_final: 0.8510 (t0) REVERT: B 22 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8721 (m) REVERT: B 76 ASN cc_start: 0.8547 (m-40) cc_final: 0.8229 (m110) REVERT: B 231 MET cc_start: 0.9280 (mtt) cc_final: 0.8986 (mtt) REVERT: B 347 LYS cc_start: 0.7921 (mttm) cc_final: 0.7719 (mttm) REVERT: B 350 GLU cc_start: 0.7184 (mp0) cc_final: 0.6922 (mp0) REVERT: B 359 MET cc_start: 0.9139 (ttm) cc_final: 0.8916 (ttp) REVERT: B 369 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8455 (mm) REVERT: C 169 PHE cc_start: 0.6667 (m-80) cc_final: 0.6336 (m-10) REVERT: C 215 ASN cc_start: 0.9069 (p0) cc_final: 0.8859 (p0) REVERT: C 366 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7242 (mttp) REVERT: C 372 GLN cc_start: 0.7309 (mm-40) cc_final: 0.7018 (mm110) REVERT: D 16 ASP cc_start: 0.8131 (m-30) cc_final: 0.7613 (m-30) REVERT: D 20 ASP cc_start: 0.7991 (m-30) cc_final: 0.7623 (m-30) REVERT: D 271 MET cc_start: 0.8961 (mtp) cc_final: 0.8707 (mtm) REVERT: D 348 ARG cc_start: 0.7911 (ptt-90) cc_final: 0.7199 (ptp-110) REVERT: E 62 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7452 (mp0) REVERT: E 68 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7222 (pp20) REVERT: F 39 MET cc_start: 0.9162 (mtt) cc_final: 0.8622 (mtm) REVERT: H 9 ASP cc_start: 0.8135 (m-30) cc_final: 0.7825 (m-30) REVERT: H 31 MET cc_start: 0.8839 (ttp) cc_final: 0.8456 (ttp) REVERT: I 30 ARG cc_start: 0.7438 (mtt-85) cc_final: 0.6759 (mmt90) REVERT: K 22 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: L 23 LEU cc_start: 0.8087 (mt) cc_final: 0.7839 (mp) REVERT: M 6 LEU cc_start: 0.8662 (mp) cc_final: 0.8364 (mm) REVERT: T 16 VAL cc_start: 0.7581 (t) cc_final: 0.6934 (p) outliers start: 18 outliers final: 10 residues processed: 210 average time/residue: 0.6709 time to fit residues: 157.0804 Evaluate side-chains 213 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 100 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 174 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104330 restraints weight = 22089.408| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.45 r_work: 0.3029 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 19507 Z= 0.123 Angle : 0.545 9.016 26879 Z= 0.255 Chirality : 0.042 0.240 2553 Planarity : 0.004 0.051 3320 Dihedral : 16.232 123.452 3653 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.10 % Allowed : 13.55 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.20), residues: 1866 helix: 2.00 (0.16), residues: 1106 sheet: -0.87 (0.71), residues: 47 loop : 0.22 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.012 0.001 TYR B 273 PHE 0.028 0.001 PHE B 246 TRP 0.015 0.001 TRP A 131 HIS 0.006 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00275 (19474) covalent geometry : angle 0.54466 (26879) hydrogen bonds : bond 0.04003 ( 863) hydrogen bonds : angle 4.25669 ( 2427) Misc. bond : bond 0.02798 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6442.49 seconds wall clock time: 110 minutes 19.67 seconds (6619.67 seconds total)