Starting phenix.real_space_refine on Wed Nov 19 05:18:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c1g_7330/11_2025/6c1g_7330.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c1g_7330/11_2025/6c1g_7330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c1g_7330/11_2025/6c1g_7330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c1g_7330/11_2025/6c1g_7330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c1g_7330/11_2025/6c1g_7330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c1g_7330/11_2025/6c1g_7330.map" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 126 5.16 5 C 13115 2.51 5 N 3630 2.21 5 O 4105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20994 Number of models: 1 Model: "" Number of chains: 13 Chain: "P" Number of atoms: 5570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5570 Classifications: {'peptide': 729} Incomplete info: {'backbone_only': 71, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 700} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'TYR:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6, 'GLN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 185 Chain: "R" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 591 Classifications: {'peptide': 148} Incomplete info: {'backbone_only': 136, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 143} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 842 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'ASP:plan': 17, 'GLN:plan1': 6, 'GLU:plan': 21, 'PHE:plan': 8, 'ARG:plan': 6, 'ASN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 308 Chain: "A" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.11, per 1000 atoms: 0.24 Number of scatterers: 20994 At special positions: 0 Unit cell: (201.5, 106.6, 193.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 126 16.00 P 12 15.00 Mg 6 11.99 O 4105 8.00 N 3630 7.00 C 13115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 975.6 milliseconds 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 36 sheets defined 49.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'P' and resid 28 through 41 Processing helix chain 'P' and resid 61 through 64 removed outlier: 3.708A pdb=" N TYR P 64 " --> pdb=" O LEU P 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 64' Processing helix chain 'P' and resid 65 through 73 removed outlier: 3.532A pdb=" N TYR P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 97 removed outlier: 3.537A pdb=" N SER P 88 " --> pdb=" O ILE P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 130 removed outlier: 4.090A pdb=" N GLY P 130 " --> pdb=" O ALA P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 132 through 153 removed outlier: 4.222A pdb=" N VAL P 138 " --> pdb=" O GLU P 134 " (cutoff:3.500A) Proline residue: P 147 - end of helix Processing helix chain 'P' and resid 192 through 197 removed outlier: 4.088A pdb=" N VAL P 196 " --> pdb=" O LYS P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 215 removed outlier: 4.207A pdb=" N TYR P 209 " --> pdb=" O PHE P 205 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA P 215 " --> pdb=" O LEU P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 216 through 223 Processing helix chain 'P' and resid 236 through 240 removed outlier: 3.725A pdb=" N SER P 239 " --> pdb=" O SER P 236 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA P 240 " --> pdb=" O LEU P 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 236 through 240' Processing helix chain 'P' and resid 246 through 261 removed outlier: 4.025A pdb=" N ASN P 250 " --> pdb=" O ASP P 246 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN P 259 " --> pdb=" O ARG P 255 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE P 260 " --> pdb=" O ASN P 256 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL P 261 " --> pdb=" O ALA P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 282 removed outlier: 3.960A pdb=" N GLU P 269 " --> pdb=" O ASP P 265 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL P 274 " --> pdb=" O SER P 270 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY P 282 " --> pdb=" O VAL P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 313 Processing helix chain 'P' and resid 316 through 325 removed outlier: 3.586A pdb=" N LEU P 320 " --> pdb=" O ASP P 316 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER P 325 " --> pdb=" O GLU P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 373 removed outlier: 4.433A pdb=" N SER P 371 " --> pdb=" O ARG P 367 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE P 372 " --> pdb=" O ILE P 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 398 through 430 removed outlier: 3.598A pdb=" N GLU P 430 " --> pdb=" O GLU P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 442 through 451 removed outlier: 3.526A pdb=" N ASP P 447 " --> pdb=" O ALA P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 466 Processing helix chain 'P' and resid 471 through 483 removed outlier: 3.647A pdb=" N PHE P 475 " --> pdb=" O THR P 471 " (cutoff:3.500A) Processing helix chain 'P' and resid 525 through 531 Processing helix chain 'P' and resid 535 through 544 removed outlier: 3.647A pdb=" N SER P 539 " --> pdb=" O TYR P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 547 through 554 Processing helix chain 'P' and resid 555 through 558 removed outlier: 4.136A pdb=" N ASN P 558 " --> pdb=" O PRO P 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 555 through 558' Processing helix chain 'P' and resid 569 through 586 Processing helix chain 'P' and resid 608 through 620 removed outlier: 3.550A pdb=" N VAL P 612 " --> pdb=" O SER P 608 " (cutoff:3.500A) Processing helix chain 'P' and resid 620 through 629 removed outlier: 3.713A pdb=" N ARG P 626 " --> pdb=" O LEU P 622 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL P 627 " --> pdb=" O GLU P 623 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG P 628 " --> pdb=" O ASN P 624 " (cutoff:3.500A) Processing helix chain 'P' and resid 638 through 646 Processing helix chain 'P' and resid 659 through 671 Processing helix chain 'P' and resid 689 through 729 removed outlier: 4.289A pdb=" N LEU P 693 " --> pdb=" O ASN P 689 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU P 705 " --> pdb=" O LYS P 701 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE P 714 " --> pdb=" O LEU P 710 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY P 729 " --> pdb=" O LEU P 725 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 19 removed outlier: 3.755A pdb=" N GLU R 14 " --> pdb=" O ALA R 10 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA R 15 " --> pdb=" O GLU R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 39 removed outlier: 4.062A pdb=" N VAL R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 56 removed outlier: 3.875A pdb=" N VAL R 55 " --> pdb=" O MET R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 81 through 92 removed outlier: 4.351A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 110 Processing helix chain 'R' and resid 117 through 129 removed outlier: 3.558A pdb=" N ARG R 126 " --> pdb=" O ASP R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 removed outlier: 3.892A pdb=" N GLN R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.895A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.662A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 263 Proline residue: A 258 - end of helix removed outlier: 4.723A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.502A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.994A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.896A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.662A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix removed outlier: 4.723A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.502A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.995A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 368 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.896A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.662A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 263 Proline residue: C 258 - end of helix removed outlier: 4.723A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.502A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.993A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 368 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.896A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.661A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 263 Proline residue: D 258 - end of helix removed outlier: 4.723A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.502A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.994A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 368 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.896A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.662A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 263 Proline residue: E 258 - end of helix removed outlier: 4.724A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.501A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.995A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 368 through 374 Processing sheet with id=AA1, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.534A pdb=" N VAL P 52 " --> pdb=" O ARG P 594 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE P 596 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER P 54 " --> pdb=" O ILE P 596 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS P 103 " --> pdb=" O ASN P 591 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE P 593 " --> pdb=" O CYS P 103 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU P 105 " --> pdb=" O ILE P 593 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N CYS P 595 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR P 107 " --> pdb=" O CYS P 595 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN P 102 " --> pdb=" O GLY P 384 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LEU P 386 " --> pdb=" O GLN P 102 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE P 104 " --> pdb=" O LEU P 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 286 through 288 Processing sheet with id=AA3, first strand: chain 'P' and resid 326 through 330 Processing sheet with id=AA4, first strand: chain 'P' and resid 489 through 490 Processing sheet with id=AA5, first strand: chain 'P' and resid 634 through 637 Processing sheet with id=AA6, first strand: chain 'R' and resid 99 through 101 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.000A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.039A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.001A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.039A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.000A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.040A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.001A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.040A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.000A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.040A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 238 through 241 1023 hydrogen bonds defined for protein. 2862 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: 4.38 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6996 1.34 - 1.46: 4393 1.46 - 1.58: 9789 1.58 - 1.70: 17 1.70 - 1.82: 216 Bond restraints: 21411 Sorted by residual: bond pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sigma weight residual 1.610 1.469 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" O1A ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sigma weight residual 1.510 1.427 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP B 401 " pdb=" N7 ADP B 401 " ideal model delta sigma weight residual 1.350 1.414 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 21406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 28878 6.76 - 13.51: 40 13.51 - 20.27: 0 20.27 - 27.02: 1 27.02 - 33.78: 1 Bond angle restraints: 28920 Sorted by residual: angle pdb=" CG ARG D 95 " pdb=" CD ARG D 95 " pdb=" NE ARG D 95 " ideal model delta sigma weight residual 112.00 145.78 -33.78 2.20e+00 2.07e-01 2.36e+02 angle pdb=" O1B ADP B 401 " pdb=" PB ADP B 401 " pdb=" O3B ADP B 401 " ideal model delta sigma weight residual 119.90 98.31 21.59 3.00e+00 1.11e-01 5.18e+01 angle pdb=" C ASP R 2 " pdb=" N GLN R 3 " pdb=" CA GLN R 3 " ideal model delta sigma weight residual 121.70 132.32 -10.62 1.80e+00 3.09e-01 3.48e+01 angle pdb=" C GLN R 3 " pdb=" N LEU R 4 " pdb=" CA LEU R 4 " ideal model delta sigma weight residual 121.31 129.38 -8.07 1.49e+00 4.50e-01 2.93e+01 angle pdb=" C GLY E 302 " pdb=" N THR E 303 " pdb=" CA THR E 303 " ideal model delta sigma weight residual 120.38 127.55 -7.17 1.46e+00 4.69e-01 2.41e+01 ... (remaining 28915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.00: 12287 21.00 - 42.01: 277 42.01 - 63.01: 40 63.01 - 84.02: 10 84.02 - 105.02: 4 Dihedral angle restraints: 12618 sinusoidal: 5053 harmonic: 7565 Sorted by residual: dihedral pdb=" CA GLU P 24 " pdb=" C GLU P 24 " pdb=" N PRO P 25 " pdb=" CA PRO P 25 " ideal model delta harmonic sigma weight residual 180.00 -107.06 -72.94 0 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA GLU A 361 " pdb=" C GLU A 361 " pdb=" N TYR A 362 " pdb=" CA TYR A 362 " ideal model delta harmonic sigma weight residual 180.00 144.72 35.28 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" CA GLU C 361 " pdb=" C GLU C 361 " pdb=" N TYR C 362 " pdb=" CA TYR C 362 " ideal model delta harmonic sigma weight residual 180.00 144.75 35.25 0 5.00e+00 4.00e-02 4.97e+01 ... (remaining 12615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2214 0.053 - 0.105: 644 0.105 - 0.158: 182 0.158 - 0.211: 27 0.211 - 0.263: 10 Chirality restraints: 3077 Sorted by residual: chirality pdb=" CB ILE E 71 " pdb=" CA ILE E 71 " pdb=" CG1 ILE E 71 " pdb=" CG2 ILE E 71 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE C 71 " pdb=" CA ILE C 71 " pdb=" CG1 ILE C 71 " pdb=" CG2 ILE C 71 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE D 71 " pdb=" CA ILE D 71 " pdb=" CG1 ILE D 71 " pdb=" CG2 ILE D 71 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 3074 not shown) Planarity restraints: 3803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 401 " 0.052 2.00e-02 2.50e+03 7.82e-02 1.68e+02 pdb=" C2 ADP B 401 " -0.021 2.00e-02 2.50e+03 pdb=" C4 ADP B 401 " 0.019 2.00e-02 2.50e+03 pdb=" C5 ADP B 401 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ADP B 401 " -0.010 2.00e-02 2.50e+03 pdb=" C8 ADP B 401 " -0.105 2.00e-02 2.50e+03 pdb=" N1 ADP B 401 " -0.155 2.00e-02 2.50e+03 pdb=" N3 ADP B 401 " 0.079 2.00e-02 2.50e+03 pdb=" N6 ADP B 401 " 0.146 2.00e-02 2.50e+03 pdb=" N7 ADP B 401 " -0.024 2.00e-02 2.50e+03 pdb=" N9 ADP B 401 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU P 24 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO P 25 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO P 25 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO P 25 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 359 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C LYS B 359 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS B 359 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN B 360 " 0.023 2.00e-02 2.50e+03 ... (remaining 3800 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 78 2.40 - 3.02: 10735 3.02 - 3.65: 31810 3.65 - 4.27: 49283 4.27 - 4.90: 82439 Nonbonded interactions: 174345 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 1.770 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.872 2.170 nonbonded pdb=" CD2 LEU P 142 " pdb=" SD MET P 170 " model vdw 2.011 3.820 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.091 2.170 nonbonded pdb="MG MG P 801 " pdb=" O2B ADP P 802 " model vdw 2.102 2.170 ... (remaining 174340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.120 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 21411 Z= 0.277 Angle : 0.979 33.777 28920 Z= 0.552 Chirality : 0.056 0.263 3077 Planarity : 0.007 0.104 3803 Dihedral : 10.059 105.020 7904 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.51 % Allowed : 2.21 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % Twisted General : 0.38 % 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: -3.41 (0.13), residues: 2738 helix: -2.71 (0.10), residues: 1197 sheet: -1.33 (0.25), residues: 389 loop : -1.88 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 511 TYR 0.030 0.003 TYR C 294 PHE 0.024 0.003 PHE C 124 TRP 0.031 0.004 TRP A 340 HIS 0.008 0.002 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00599 (21411) covalent geometry : angle 0.97867 (28920) hydrogen bonds : bond 0.13902 ( 1013) hydrogen bonds : angle 9.67270 ( 2862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 444 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 485 THR cc_start: 0.7512 (p) cc_final: 0.7149 (t) REVERT: B 305 MET cc_start: 0.7389 (mmm) cc_final: 0.6433 (mmt) REVERT: C 44 MET cc_start: 0.8008 (mmm) cc_final: 0.7720 (mmm) outliers start: 11 outliers final: 0 residues processed: 454 average time/residue: 0.1900 time to fit residues: 124.5468 Evaluate side-chains 194 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 ASN P 141 GLN P 293 ASN P 304 ASN ** P 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 531 ASN P 563 ASN P 573 GLN P 624 ASN A 59 GLN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN B 162 ASN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 115 ASN C 162 ASN C 297 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 173 HIS D 314 GLN E 115 ASN E 121 GLN E 162 ASN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 360 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054885 restraints weight = 113206.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056299 restraints weight = 56748.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.057274 restraints weight = 34709.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057872 restraints weight = 24168.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.058315 restraints weight = 18704.725| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 21411 Z= 0.148 Angle : 0.687 8.421 28920 Z= 0.351 Chirality : 0.046 0.178 3077 Planarity : 0.005 0.092 3803 Dihedral : 7.140 77.479 3050 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.15 % Allowed : 9.86 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: -1.20 (0.15), residues: 2738 helix: -0.25 (0.14), residues: 1164 sheet: -0.73 (0.25), residues: 406 loop : -1.27 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 231 TYR 0.020 0.002 TYR A 294 PHE 0.022 0.002 PHE D 124 TRP 0.014 0.002 TRP D 86 HIS 0.007 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00324 (21411) covalent geometry : angle 0.68679 (28920) hydrogen bonds : bond 0.03637 ( 1013) hydrogen bonds : angle 5.70675 ( 2862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 93 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8404 (ptt180) REVERT: P 122 MET cc_start: 0.8988 (mmt) cc_final: 0.8671 (mmt) REVERT: P 171 ASP cc_start: 0.8633 (m-30) cc_final: 0.7963 (m-30) REVERT: P 173 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: P 192 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8543 (mtpt) REVERT: P 258 MET cc_start: 0.8558 (ppp) cc_final: 0.8132 (ppp) REVERT: P 356 LEU cc_start: 0.9520 (tp) cc_final: 0.9194 (pp) REVERT: P 485 THR cc_start: 0.8660 (p) cc_final: 0.8353 (t) REVERT: P 520 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9121 (tp) REVERT: A 190 MET cc_start: 0.8583 (mtt) cc_final: 0.8255 (mtt) REVERT: B 61 LYS cc_start: 0.9288 (mttm) cc_final: 0.8828 (mttm) REVERT: B 132 MET cc_start: 0.8933 (ptm) cc_final: 0.8727 (ppp) REVERT: B 300 SER cc_start: 0.6766 (t) cc_final: 0.6479 (t) REVERT: B 305 MET cc_start: 0.8743 (mmm) cc_final: 0.8419 (mmt) REVERT: C 44 MET cc_start: 0.9046 (mmm) cc_final: 0.8686 (mmm) REVERT: D 44 MET cc_start: 0.8659 (mmm) cc_final: 0.8336 (mmm) REVERT: D 176 MET cc_start: 0.8727 (tpp) cc_final: 0.8343 (mpp) REVERT: E 195 GLU cc_start: 0.8269 (tt0) cc_final: 0.8043 (tp30) REVERT: E 227 MET cc_start: 0.9289 (mmm) cc_final: 0.8969 (mmm) REVERT: E 305 MET cc_start: 0.8163 (mmm) cc_final: 0.7886 (mmm) outliers start: 25 outliers final: 8 residues processed: 232 average time/residue: 0.1618 time to fit residues: 58.3118 Evaluate side-chains 177 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 292 MET Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 585 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain E residue 56 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 3 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 41 HIS ** P 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 198 GLN ** P 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 317 GLN ** P 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 436 HIS ** P 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 689 ASN A 128 ASN A 297 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 41 GLN E 40 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040594 restraints weight = 120084.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.041938 restraints weight = 58976.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.042796 restraints weight = 35493.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043333 restraints weight = 24730.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.043700 restraints weight = 19261.920| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.174 21411 Z= 0.363 Angle : 0.830 9.928 28920 Z= 0.427 Chirality : 0.048 0.188 3077 Planarity : 0.006 0.088 3803 Dihedral : 7.419 80.658 3050 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.84 % Allowed : 10.78 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2738 helix: 0.52 (0.15), residues: 1193 sheet: -0.73 (0.25), residues: 428 loop : -0.96 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 62 TYR 0.019 0.002 TYR C 53 PHE 0.021 0.003 PHE C 124 TRP 0.020 0.003 TRP E 79 HIS 0.009 0.002 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00782 (21411) covalent geometry : angle 0.82996 (28920) hydrogen bonds : bond 0.04224 ( 1013) hydrogen bonds : angle 5.60553 ( 2862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 122 MET cc_start: 0.9121 (mmt) cc_final: 0.8684 (mmt) REVERT: P 173 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: P 258 MET cc_start: 0.8711 (ppp) cc_final: 0.7915 (ppp) REVERT: A 28 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7570 (ttp80) REVERT: B 300 SER cc_start: 0.6869 (t) cc_final: 0.6502 (t) REVERT: B 305 MET cc_start: 0.8753 (mmm) cc_final: 0.8350 (mmt) REVERT: C 299 MET cc_start: 0.8136 (ttp) cc_final: 0.7836 (ptt) REVERT: D 44 MET cc_start: 0.8727 (mmm) cc_final: 0.8504 (mmm) REVERT: D 176 MET cc_start: 0.8757 (tpp) cc_final: 0.8347 (mpp) REVERT: D 283 MET cc_start: 0.8922 (mmp) cc_final: 0.8714 (mmp) REVERT: D 334 GLU cc_start: 0.6951 (mp0) cc_final: 0.6270 (mp0) REVERT: E 10 CYS cc_start: 0.9063 (t) cc_final: 0.8807 (t) REVERT: E 132 MET cc_start: 0.8087 (ptm) cc_final: 0.7813 (ppp) REVERT: E 227 MET cc_start: 0.9104 (mmm) cc_final: 0.8839 (mmm) REVERT: E 305 MET cc_start: 0.8727 (mmm) cc_final: 0.8391 (tpp) outliers start: 40 outliers final: 20 residues processed: 189 average time/residue: 0.1371 time to fit residues: 42.3229 Evaluate side-chains 169 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain P residue 523 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 194 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 253 optimal weight: 1.9990 chunk 70 optimal weight: 30.0000 chunk 247 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 76 ASN P 206 HIS P 344 GLN ** P 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN A 297 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 101 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.056901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042555 restraints weight = 117425.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.043911 restraints weight = 57328.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.044804 restraints weight = 34640.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.045367 restraints weight = 24050.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.045765 restraints weight = 18639.181| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21411 Z= 0.136 Angle : 0.635 8.836 28920 Z= 0.316 Chirality : 0.044 0.180 3077 Planarity : 0.004 0.080 3803 Dihedral : 6.936 75.722 3050 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.06 % Allowed : 12.11 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2738 helix: 1.17 (0.15), residues: 1177 sheet: -0.50 (0.26), residues: 406 loop : -0.70 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.016 0.001 TYR C 294 PHE 0.012 0.001 PHE P 694 TRP 0.011 0.002 TRP E 86 HIS 0.006 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00302 (21411) covalent geometry : angle 0.63510 (28920) hydrogen bonds : bond 0.03037 ( 1013) hydrogen bonds : angle 5.11269 ( 2862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 122 MET cc_start: 0.9138 (mmt) cc_final: 0.8718 (mmt) REVERT: P 173 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: P 258 MET cc_start: 0.8438 (ppp) cc_final: 0.7855 (ppp) REVERT: B 305 MET cc_start: 0.8709 (mmm) cc_final: 0.8350 (mmt) REVERT: C 227 MET cc_start: 0.9356 (mmm) cc_final: 0.9010 (mmm) REVERT: D 176 MET cc_start: 0.8623 (tpp) cc_final: 0.8184 (mpp) REVERT: D 283 MET cc_start: 0.8792 (mmp) cc_final: 0.8462 (mmp) REVERT: D 334 GLU cc_start: 0.7509 (mp0) cc_final: 0.6986 (mp0) REVERT: E 10 CYS cc_start: 0.8941 (t) cc_final: 0.8580 (t) REVERT: E 132 MET cc_start: 0.8058 (ptm) cc_final: 0.7665 (ppp) REVERT: E 227 MET cc_start: 0.8980 (mmm) cc_final: 0.8595 (mmm) REVERT: E 269 MET cc_start: 0.8359 (ttp) cc_final: 0.7799 (ptm) outliers start: 23 outliers final: 10 residues processed: 173 average time/residue: 0.1346 time to fit residues: 38.9675 Evaluate side-chains 158 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 56 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 234 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 78 optimal weight: 0.0020 chunk 115 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 344 GLN ** P 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.055993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041733 restraints weight = 117822.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.043055 restraints weight = 57689.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.043927 restraints weight = 34975.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.044488 restraints weight = 24382.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.044864 restraints weight = 18912.032| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21411 Z= 0.190 Angle : 0.650 9.023 28920 Z= 0.324 Chirality : 0.044 0.157 3077 Planarity : 0.004 0.077 3803 Dihedral : 6.697 75.345 3050 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.24 % Allowed : 12.11 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.36 (0.17), residues: 2738 helix: 1.40 (0.15), residues: 1177 sheet: -0.37 (0.27), residues: 358 loop : -0.68 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 566 TYR 0.016 0.001 TYR B 143 PHE 0.025 0.002 PHE P 415 TRP 0.016 0.002 TRP E 86 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00417 (21411) covalent geometry : angle 0.65023 (28920) hydrogen bonds : bond 0.03076 ( 1013) hydrogen bonds : angle 5.02112 ( 2862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 122 MET cc_start: 0.9205 (mmt) cc_final: 0.8919 (mmt) REVERT: P 170 MET cc_start: 0.8514 (mtm) cc_final: 0.8269 (tmm) REVERT: P 173 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: P 258 MET cc_start: 0.8488 (ppp) cc_final: 0.7551 (ppp) REVERT: B 100 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8194 (pp20) REVERT: B 305 MET cc_start: 0.8730 (mmm) cc_final: 0.8419 (mmt) REVERT: C 334 GLU cc_start: 0.7700 (mp0) cc_final: 0.7111 (mp0) REVERT: D 176 MET cc_start: 0.8582 (tpp) cc_final: 0.8150 (mpp) REVERT: D 283 MET cc_start: 0.8844 (mmp) cc_final: 0.8509 (mmp) REVERT: D 299 MET cc_start: 0.8139 (ttp) cc_final: 0.7732 (ptp) REVERT: E 10 CYS cc_start: 0.8911 (t) cc_final: 0.8528 (t) REVERT: E 132 MET cc_start: 0.8049 (ptm) cc_final: 0.7605 (ppp) REVERT: E 227 MET cc_start: 0.8996 (mmm) cc_final: 0.8652 (mmm) REVERT: E 287 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8720 (mt) REVERT: E 305 MET cc_start: 0.8865 (mmm) cc_final: 0.8588 (tpp) outliers start: 27 outliers final: 16 residues processed: 168 average time/residue: 0.1372 time to fit residues: 38.0332 Evaluate side-chains 163 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 287 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.057413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.043151 restraints weight = 116536.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.044519 restraints weight = 56864.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.045391 restraints weight = 34249.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.045972 restraints weight = 23802.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.046332 restraints weight = 18366.630| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21411 Z= 0.108 Angle : 0.605 11.160 28920 Z= 0.296 Chirality : 0.043 0.165 3077 Planarity : 0.004 0.073 3803 Dihedral : 6.319 69.180 3050 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.01 % Allowed : 12.16 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.60 (0.17), residues: 2738 helix: 1.61 (0.16), residues: 1176 sheet: -0.30 (0.27), residues: 358 loop : -0.55 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 566 TYR 0.016 0.001 TYR B 143 PHE 0.019 0.001 PHE P 415 TRP 0.013 0.001 TRP P 363 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00238 (21411) covalent geometry : angle 0.60529 (28920) hydrogen bonds : bond 0.02675 ( 1013) hydrogen bonds : angle 4.80927 ( 2862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 122 MET cc_start: 0.9202 (mmt) cc_final: 0.8857 (mmt) REVERT: P 170 MET cc_start: 0.8382 (mtm) cc_final: 0.8155 (tmm) REVERT: P 173 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: P 258 MET cc_start: 0.8484 (ppp) cc_final: 0.7746 (ppp) REVERT: P 356 LEU cc_start: 0.9542 (tp) cc_final: 0.9244 (pp) REVERT: A 44 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7783 (tpt) REVERT: A 299 MET cc_start: 0.8462 (ptm) cc_final: 0.7413 (ppp) REVERT: B 123 MET cc_start: 0.8711 (tpp) cc_final: 0.8397 (tpp) REVERT: B 305 MET cc_start: 0.8722 (mmm) cc_final: 0.8443 (mmt) REVERT: C 227 MET cc_start: 0.9317 (mmm) cc_final: 0.9057 (mmm) REVERT: D 47 MET cc_start: 0.7746 (ptm) cc_final: 0.7466 (ptm) REVERT: D 119 MET cc_start: 0.8993 (ttm) cc_final: 0.8785 (ttm) REVERT: D 176 MET cc_start: 0.8455 (tpp) cc_final: 0.8091 (mpp) REVERT: D 283 MET cc_start: 0.8749 (mmp) cc_final: 0.8442 (mmm) REVERT: E 10 CYS cc_start: 0.8836 (t) cc_final: 0.8437 (t) REVERT: E 47 MET cc_start: 0.7925 (ptm) cc_final: 0.7655 (ptm) REVERT: E 176 MET cc_start: 0.7193 (tpp) cc_final: 0.6535 (mpp) REVERT: E 227 MET cc_start: 0.8928 (mmm) cc_final: 0.8641 (mmm) REVERT: E 269 MET cc_start: 0.8367 (ttp) cc_final: 0.7844 (ptm) REVERT: E 287 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8764 (mt) REVERT: E 305 MET cc_start: 0.8952 (mmm) cc_final: 0.8707 (tpp) outliers start: 22 outliers final: 12 residues processed: 170 average time/residue: 0.1409 time to fit residues: 39.5418 Evaluate side-chains 163 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 287 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 158 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 229 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 13 ASN P 160 ASN ** P 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.055672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.041472 restraints weight = 119007.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042787 restraints weight = 58029.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043616 restraints weight = 35160.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.044184 restraints weight = 24673.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044555 restraints weight = 19148.501| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 21411 Z= 0.210 Angle : 0.657 9.333 28920 Z= 0.324 Chirality : 0.044 0.263 3077 Planarity : 0.004 0.072 3803 Dihedral : 6.378 70.197 3050 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.34 % Allowed : 12.30 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.63 (0.17), residues: 2738 helix: 1.62 (0.15), residues: 1175 sheet: -0.31 (0.28), residues: 360 loop : -0.51 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 566 TYR 0.014 0.001 TYR B 143 PHE 0.017 0.001 PHE P 415 TRP 0.015 0.002 TRP E 79 HIS 0.006 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00462 (21411) covalent geometry : angle 0.65711 (28920) hydrogen bonds : bond 0.02989 ( 1013) hydrogen bonds : angle 4.89437 ( 2862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 122 MET cc_start: 0.9209 (mmt) cc_final: 0.8853 (mmt) REVERT: P 170 MET cc_start: 0.8499 (mtm) cc_final: 0.8170 (tmm) REVERT: P 173 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8593 (pm20) REVERT: P 258 MET cc_start: 0.8457 (ppp) cc_final: 0.7692 (ppp) REVERT: P 389 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6722 (p90) REVERT: B 105 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9246 (mm) REVERT: B 123 MET cc_start: 0.8751 (tpp) cc_final: 0.8427 (tpp) REVERT: B 305 MET cc_start: 0.8735 (mmm) cc_final: 0.8455 (mmt) REVERT: C 227 MET cc_start: 0.9347 (mmm) cc_final: 0.9139 (mmm) REVERT: C 334 GLU cc_start: 0.7579 (mp0) cc_final: 0.7054 (mp0) REVERT: D 176 MET cc_start: 0.8579 (tpp) cc_final: 0.8142 (mpp) REVERT: D 305 MET cc_start: 0.8185 (ptp) cc_final: 0.7342 (mtm) REVERT: E 10 CYS cc_start: 0.8882 (t) cc_final: 0.8503 (t) REVERT: E 47 MET cc_start: 0.7983 (ptm) cc_final: 0.7676 (ptm) REVERT: E 132 MET cc_start: 0.8077 (ptm) cc_final: 0.7564 (ppp) REVERT: E 227 MET cc_start: 0.8999 (mmm) cc_final: 0.8669 (mmm) REVERT: E 269 MET cc_start: 0.8400 (ttp) cc_final: 0.7845 (ptm) REVERT: E 287 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8641 (mt) REVERT: E 305 MET cc_start: 0.9004 (mmm) cc_final: 0.8750 (tpp) outliers start: 29 outliers final: 18 residues processed: 166 average time/residue: 0.1491 time to fit residues: 40.5117 Evaluate side-chains 165 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 389 TYR Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 287 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 112 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 133 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.057394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.043199 restraints weight = 116830.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.044552 restraints weight = 56968.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.045421 restraints weight = 34307.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.045972 restraints weight = 23889.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.046366 restraints weight = 18519.700| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21411 Z= 0.107 Angle : 0.620 13.368 28920 Z= 0.299 Chirality : 0.043 0.226 3077 Planarity : 0.004 0.068 3803 Dihedral : 6.093 66.017 3050 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.06 % Allowed : 12.62 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.80 (0.17), residues: 2738 helix: 1.77 (0.16), residues: 1176 sheet: -0.22 (0.28), residues: 345 loop : -0.42 (0.19), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 335 TYR 0.014 0.001 TYR B 143 PHE 0.017 0.001 PHE P 415 TRP 0.012 0.001 TRP P 363 HIS 0.004 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00239 (21411) covalent geometry : angle 0.61991 (28920) hydrogen bonds : bond 0.02613 ( 1013) hydrogen bonds : angle 4.70215 ( 2862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 122 MET cc_start: 0.9180 (mmt) cc_final: 0.8811 (mmt) REVERT: P 173 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: P 258 MET cc_start: 0.8388 (ppp) cc_final: 0.7741 (ppp) REVERT: P 356 LEU cc_start: 0.9545 (tp) cc_final: 0.9248 (pp) REVERT: P 389 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6619 (p90) REVERT: B 123 MET cc_start: 0.8701 (tpp) cc_final: 0.8401 (tpp) REVERT: B 305 MET cc_start: 0.8715 (mmm) cc_final: 0.8435 (mmt) REVERT: C 334 GLU cc_start: 0.7519 (mp0) cc_final: 0.6940 (mp0) REVERT: D 176 MET cc_start: 0.8441 (tpp) cc_final: 0.8110 (mpp) REVERT: D 334 GLU cc_start: 0.7310 (mp0) cc_final: 0.6943 (pm20) REVERT: E 10 CYS cc_start: 0.8808 (t) cc_final: 0.8445 (t) REVERT: E 47 MET cc_start: 0.7899 (ptm) cc_final: 0.7587 (ptm) REVERT: E 132 MET cc_start: 0.8077 (ptm) cc_final: 0.7521 (ppp) REVERT: E 227 MET cc_start: 0.8916 (mmm) cc_final: 0.8660 (mmm) REVERT: E 269 MET cc_start: 0.8365 (ttp) cc_final: 0.7902 (ptm) REVERT: E 287 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8682 (mt) REVERT: E 305 MET cc_start: 0.9009 (mmm) cc_final: 0.8757 (tpp) outliers start: 23 outliers final: 13 residues processed: 174 average time/residue: 0.1462 time to fit residues: 41.5598 Evaluate side-chains 164 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 389 TYR Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 287 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 200 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 76 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 126 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.057837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043640 restraints weight = 117545.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.044994 restraints weight = 57054.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.045849 restraints weight = 34448.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.046423 restraints weight = 23999.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.046801 restraints weight = 18526.216| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21411 Z= 0.104 Angle : 0.629 12.663 28920 Z= 0.302 Chirality : 0.043 0.186 3077 Planarity : 0.004 0.064 3803 Dihedral : 5.746 58.640 3050 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 1.01 % Allowed : 12.85 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.82 (0.17), residues: 2738 helix: 1.64 (0.15), residues: 1210 sheet: -0.14 (0.29), residues: 345 loop : -0.32 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 566 TYR 0.013 0.001 TYR B 143 PHE 0.016 0.001 PHE P 415 TRP 0.013 0.001 TRP P 363 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00236 (21411) covalent geometry : angle 0.62896 (28920) hydrogen bonds : bond 0.02537 ( 1013) hydrogen bonds : angle 4.60622 ( 2862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: P 258 MET cc_start: 0.8389 (ppp) cc_final: 0.7739 (ppp) REVERT: P 356 LEU cc_start: 0.9554 (tp) cc_final: 0.9255 (pp) REVERT: P 389 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6541 (p90) REVERT: A 325 MET cc_start: 0.8621 (tpp) cc_final: 0.8332 (mmt) REVERT: B 105 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9260 (mm) REVERT: B 123 MET cc_start: 0.8694 (tpp) cc_final: 0.8403 (tpp) REVERT: B 305 MET cc_start: 0.8705 (mmm) cc_final: 0.8403 (mmt) REVERT: C 227 MET cc_start: 0.9288 (mmm) cc_final: 0.9014 (mmm) REVERT: C 334 GLU cc_start: 0.7618 (mp0) cc_final: 0.7038 (mp0) REVERT: D 176 MET cc_start: 0.8416 (tpp) cc_final: 0.8045 (mpp) REVERT: D 283 MET cc_start: 0.8412 (mmp) cc_final: 0.7776 (mmp) REVERT: D 334 GLU cc_start: 0.7333 (mp0) cc_final: 0.6971 (pm20) REVERT: E 10 CYS cc_start: 0.8903 (t) cc_final: 0.8638 (t) REVERT: E 47 MET cc_start: 0.7785 (ptm) cc_final: 0.7467 (ptm) REVERT: E 132 MET cc_start: 0.8093 (ptm) cc_final: 0.7488 (tmm) REVERT: E 176 MET cc_start: 0.7241 (tpp) cc_final: 0.6643 (mpp) REVERT: E 202 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8475 (p) REVERT: E 269 MET cc_start: 0.8326 (ttp) cc_final: 0.7935 (ptm) REVERT: E 287 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8675 (mt) outliers start: 22 outliers final: 13 residues processed: 172 average time/residue: 0.1450 time to fit residues: 40.6022 Evaluate side-chains 165 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 324 PHE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 389 TYR Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 112 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 268 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 531 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.055352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.041275 restraints weight = 118928.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.042564 restraints weight = 58038.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.043388 restraints weight = 35053.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.043967 restraints weight = 24533.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.044304 restraints weight = 18932.979| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 21411 Z= 0.239 Angle : 0.716 13.211 28920 Z= 0.352 Chirality : 0.045 0.190 3077 Planarity : 0.004 0.065 3803 Dihedral : 6.012 66.531 3050 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.15 % Allowed : 12.57 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.68 (0.17), residues: 2738 helix: 1.46 (0.15), residues: 1218 sheet: -0.22 (0.29), residues: 345 loop : -0.33 (0.19), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 566 TYR 0.019 0.002 TYR C 143 PHE 0.015 0.002 PHE P 415 TRP 0.020 0.002 TRP E 79 HIS 0.012 0.001 HIS P 614 Details of bonding type rmsd covalent geometry : bond 0.00527 (21411) covalent geometry : angle 0.71577 (28920) hydrogen bonds : bond 0.03120 ( 1013) hydrogen bonds : angle 4.87144 ( 2862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: P 258 MET cc_start: 0.8441 (ppp) cc_final: 0.7690 (ppp) REVERT: P 389 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6713 (p90) REVERT: A 299 MET cc_start: 0.8536 (ptm) cc_final: 0.7568 (ppp) REVERT: A 325 MET cc_start: 0.8754 (tpp) cc_final: 0.8449 (mmt) REVERT: B 105 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9238 (mm) REVERT: B 123 MET cc_start: 0.8793 (tpp) cc_final: 0.8462 (tpp) REVERT: B 305 MET cc_start: 0.8713 (mmm) cc_final: 0.8423 (mmt) REVERT: C 334 GLU cc_start: 0.7613 (mp0) cc_final: 0.7092 (mp0) REVERT: D 176 MET cc_start: 0.8596 (tpp) cc_final: 0.8146 (mpp) REVERT: D 283 MET cc_start: 0.8548 (mmp) cc_final: 0.8203 (mmm) REVERT: D 334 GLU cc_start: 0.7564 (mp0) cc_final: 0.7161 (pm20) REVERT: E 10 CYS cc_start: 0.8939 (t) cc_final: 0.8641 (t) REVERT: E 47 MET cc_start: 0.8010 (ptm) cc_final: 0.7680 (ptm) REVERT: E 132 MET cc_start: 0.8167 (ptm) cc_final: 0.7592 (ppp) REVERT: E 202 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8448 (p) REVERT: E 269 MET cc_start: 0.8391 (ttp) cc_final: 0.7910 (ptm) REVERT: E 287 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8278 (mt) REVERT: E 299 MET cc_start: 0.8101 (tmm) cc_final: 0.7743 (tmm) outliers start: 25 outliers final: 19 residues processed: 162 average time/residue: 0.1418 time to fit residues: 38.0323 Evaluate side-chains 165 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 190 LEU Chi-restraints excluded: chain P residue 211 LEU Chi-restraints excluded: chain P residue 260 ILE Chi-restraints excluded: chain P residue 329 VAL Chi-restraints excluded: chain P residue 389 TYR Chi-restraints excluded: chain P residue 498 ARG Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 79 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 118 optimal weight: 0.4980 chunk 1 optimal weight: 0.0770 chunk 131 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 270 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.057531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.043300 restraints weight = 117994.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.044652 restraints weight = 57138.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045519 restraints weight = 34469.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046077 restraints weight = 23986.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.046464 restraints weight = 18612.509| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21411 Z= 0.108 Angle : 0.643 12.799 28920 Z= 0.310 Chirality : 0.044 0.188 3077 Planarity : 0.004 0.060 3803 Dihedral : 5.632 63.991 3050 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.88 % Allowed : 13.17 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.27 % Twisted Proline : 0.83 % 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: 0.87 (0.17), residues: 2738 helix: 1.67 (0.15), residues: 1211 sheet: -0.21 (0.29), residues: 347 loop : -0.25 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.013 0.001 TYR C 143 PHE 0.016 0.001 PHE P 415 TRP 0.013 0.002 TRP P 363 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00244 (21411) covalent geometry : angle 0.64283 (28920) hydrogen bonds : bond 0.02589 ( 1013) hydrogen bonds : angle 4.66628 ( 2862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3484.13 seconds wall clock time: 61 minutes 19.45 seconds (3679.45 seconds total)