Starting phenix.real_space_refine on Wed Mar 4 19:06:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r8f_4759/03_2026/6r8f_4759.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r8f_4759/03_2026/6r8f_4759.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6r8f_4759/03_2026/6r8f_4759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r8f_4759/03_2026/6r8f_4759.map" model { file = "/net/cci-nas-00/data/ceres_data/6r8f_4759/03_2026/6r8f_4759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r8f_4759/03_2026/6r8f_4759.cif" } 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 66 5.16 5 C 9976 2.51 5 N 2858 2.21 5 O 2908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15810 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1797 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1779 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain breaks: 3 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 68 Chain: "K" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2940 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 19, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 9, 'TYR:plan': 1, 'ASP:plan': 9, 'ASN:plan1': 1, 'GLN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 143 Chain: "E" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 115} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 78} Link IDs: {'TRANS': 81} Chain breaks: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 82} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D, L, G Time building chain proxies: 3.21, per 1000 atoms: 0.20 Number of scatterers: 15810 At special positions: 0 Unit cell: (145.919, 160.83, 105.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 66 16.00 O 2908 8.00 N 2858 7.00 C 9976 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: 1.09 Conformation dependent library (CDL) restraints added in 605.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 124 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 122 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 124 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 122 " 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 14 sheets defined 44.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.628A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 removed outlier: 3.921A pdb=" N GLN A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 250 removed outlier: 4.232A pdb=" N LYS A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.512A pdb=" N GLU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.638A pdb=" N ASP B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 112 through 120 removed outlier: 4.342A pdb=" N ARG B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.556A pdb=" N ALA B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 209 through 252 removed outlier: 3.514A pdb=" N GLU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 241 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 53 Processing helix chain 'K' and resid 53 through 69 removed outlier: 3.500A pdb=" N TRP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 115 through 125 removed outlier: 3.521A pdb=" N GLN K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU K 124 " --> pdb=" O GLN K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 155 Processing helix chain 'K' and resid 207 through 217 Processing helix chain 'K' and resid 235 through 244 removed outlier: 3.960A pdb=" N CYS K 241 " --> pdb=" O MET K 237 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU K 243 " --> pdb=" O GLU K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 270 removed outlier: 3.943A pdb=" N LYS K 269 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 316 Processing helix chain 'K' and resid 317 through 319 No H-bonds generated for 'chain 'K' and resid 317 through 319' Processing helix chain 'K' and resid 329 through 334 removed outlier: 3.787A pdb=" N ALA K 333 " --> pdb=" O ASN K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 344 removed outlier: 3.554A pdb=" N CYS K 343 " --> pdb=" O LEU K 339 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR K 344 " --> pdb=" O LYS K 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 339 through 344' Processing helix chain 'K' and resid 344 through 369 removed outlier: 3.550A pdb=" N ARG K 348 " --> pdb=" O THR K 344 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN K 353 " --> pdb=" O GLU K 349 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA K 364 " --> pdb=" O ALA K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 401 removed outlier: 3.917A pdb=" N VAL K 399 " --> pdb=" O ARG K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 434 removed outlier: 3.798A pdb=" N ARG K 434 " --> pdb=" O ALA K 430 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 462 removed outlier: 3.729A pdb=" N PHE K 441 " --> pdb=" O ARG K 437 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG K 442 " --> pdb=" O GLU K 438 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG K 443 " --> pdb=" O ASP K 439 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN K 453 " --> pdb=" O ASP K 449 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL K 458 " --> pdb=" O ILE K 454 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER K 460 " --> pdb=" O LEU K 456 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS K 461 " --> pdb=" O GLU K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 472 removed outlier: 3.515A pdb=" N LYS K 469 " --> pdb=" O LEU K 465 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER K 470 " --> pdb=" O GLN K 466 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 493 removed outlier: 3.967A pdb=" N ARG K 481 " --> pdb=" O GLU K 477 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 485 " --> pdb=" O ARG K 481 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG K 488 " --> pdb=" O ASN K 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 93 through 112 removed outlier: 3.627A pdb=" N ALA C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.921A pdb=" N GLN C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 233 through 250 removed outlier: 4.232A pdb=" N LYS C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 283 through 311 removed outlier: 3.511A pdb=" N GLU C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.638A pdb=" N ASP D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'D' and resid 112 through 120 removed outlier: 4.341A pdb=" N ARG D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.555A pdb=" N ALA D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 209 through 252 removed outlier: 3.515A pdb=" N GLU D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL D 241 " --> pdb=" O CYS D 237 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 246 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 247 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 53 Processing helix chain 'L' and resid 53 through 69 removed outlier: 3.500A pdb=" N TRP L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'L' and resid 115 through 125 removed outlier: 3.520A pdb=" N GLN L 120 " --> pdb=" O GLU L 116 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 155 Processing helix chain 'L' and resid 207 through 217 Processing helix chain 'L' and resid 235 through 244 removed outlier: 3.961A pdb=" N CYS L 241 " --> pdb=" O MET L 237 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU L 243 " --> pdb=" O GLU L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 270 removed outlier: 3.943A pdb=" N LYS L 269 " --> pdb=" O SER L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 316 Processing helix chain 'L' and resid 317 through 319 No H-bonds generated for 'chain 'L' and resid 317 through 319' Processing helix chain 'L' and resid 329 through 334 removed outlier: 3.786A pdb=" N ALA L 333 " --> pdb=" O ASN L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 344 removed outlier: 3.553A pdb=" N CYS L 343 " --> pdb=" O LEU L 339 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR L 344 " --> pdb=" O LYS L 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 339 through 344' Processing helix chain 'L' and resid 344 through 369 removed outlier: 3.550A pdb=" N ARG L 348 " --> pdb=" O THR L 344 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN L 353 " --> pdb=" O GLU L 349 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA L 364 " --> pdb=" O ALA L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 401 removed outlier: 3.917A pdb=" N VAL L 399 " --> pdb=" O ARG L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 434 removed outlier: 3.798A pdb=" N ARG L 434 " --> pdb=" O ALA L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 462 removed outlier: 3.731A pdb=" N PHE L 441 " --> pdb=" O ARG L 437 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG L 442 " --> pdb=" O GLU L 438 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG L 443 " --> pdb=" O ASP L 439 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN L 453 " --> pdb=" O ASP L 449 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL L 458 " --> pdb=" O ILE L 454 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER L 460 " --> pdb=" O LEU L 456 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS L 461 " --> pdb=" O GLU L 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 472 removed outlier: 3.515A pdb=" N LYS L 469 " --> pdb=" O LEU L 465 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER L 470 " --> pdb=" O GLN L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 493 removed outlier: 3.968A pdb=" N ARG L 481 " --> pdb=" O GLU L 477 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 485 " --> pdb=" O ARG L 481 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG L 488 " --> pdb=" O ASN L 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 14 Processing helix chain 'E' and resid 15 through 25 removed outlier: 3.951A pdb=" N SER E 20 " --> pdb=" O PRO E 16 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 24 " --> pdb=" O SER E 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 130 removed outlier: 3.624A pdb=" N GLU E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'E' and resid 242 through 255 removed outlier: 4.035A pdb=" N UNK E 246 " --> pdb=" O UNK E 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N UNK E 255 " --> pdb=" O UNK E 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 14 Processing helix chain 'G' and resid 15 through 25 removed outlier: 3.950A pdb=" N SER G 20 " --> pdb=" O PRO G 16 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 22 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 130 removed outlier: 3.624A pdb=" N GLU G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 130 " --> pdb=" O GLN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 149 Processing helix chain 'G' and resid 242 through 255 removed outlier: 4.035A pdb=" N UNK G 246 " --> pdb=" O UNK G 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N UNK G 255 " --> pdb=" O UNK G 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 219 removed outlier: 6.621A pdb=" N SER A 76 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 41 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 39 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL A 77 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 37 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 79 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N MET A 35 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 119 " --> pdb=" O CYS A 38 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 40 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL A 117 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU A 152 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP A 120 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE A 154 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS A 122 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N CYS A 156 " --> pdb=" O HIS A 122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 169 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE A 157 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG A 167 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 131 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 92 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 128 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP B 94 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE B 130 " --> pdb=" O TRP B 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG B 96 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL B 91 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY B 30 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY B 93 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 26 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE B 27 " --> pdb=" O HIS B 57 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N HIS B 57 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 29 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER B 4 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ILE B 56 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'K' and resid 134 through 136 removed outlier: 3.909A pdb=" N ILE K 273 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR K 275 " --> pdb=" O ALA K 250 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU K 220 " --> pdb=" O ARG K 160 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU K 164 " --> pdb=" O ILE K 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 296 through 297 removed outlier: 4.029A pdb=" N LYS K 297 " --> pdb=" O ILE K 307 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE K 307 " --> pdb=" O LYS K 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 371 through 372 removed outlier: 4.415A pdb=" N SER K 371 " --> pdb=" O ASP K 385 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 216 through 219 removed outlier: 6.620A pdb=" N SER C 76 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 41 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 39 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL C 77 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 37 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE C 79 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N MET C 35 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY C 119 " --> pdb=" O CYS C 38 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY C 40 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL C 117 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU C 152 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP C 120 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 154 " --> pdb=" O TRP C 120 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS C 122 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N CYS C 156 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 169 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE C 157 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 167 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 168 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 131 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 92 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU D 128 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP D 94 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE D 130 " --> pdb=" O TRP D 94 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG D 96 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL D 91 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLY D 30 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY D 93 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 26 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE D 27 " --> pdb=" O HIS D 57 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N HIS D 57 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 29 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER D 4 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ILE D 56 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AA8, first strand: chain 'L' and resid 134 through 136 removed outlier: 3.909A pdb=" N ILE L 273 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 275 " --> pdb=" O ALA L 250 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU L 220 " --> pdb=" O ARG L 160 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU L 164 " --> pdb=" O ILE L 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 296 through 297 removed outlier: 4.029A pdb=" N LYS L 297 " --> pdb=" O ILE L 307 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE L 307 " --> pdb=" O LYS L 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 371 through 372 removed outlier: 4.415A pdb=" N SER L 371 " --> pdb=" O ASP L 385 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AB3, first strand: chain 'E' and resid 160 through 163 removed outlier: 3.953A pdb=" N UNK E 179 " --> pdb=" O UNK E 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK E 203 " --> pdb=" O UNK E 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AB5, first strand: chain 'G' and resid 160 through 163 removed outlier: 3.953A pdb=" N UNK G 179 " --> pdb=" O UNK G 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N UNK G 203 " --> pdb=" O UNK G 179 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5022 1.33 - 1.45: 3003 1.45 - 1.58: 7965 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 16080 Sorted by residual: bond pdb=" CA SER B 182 " pdb=" CB SER B 182 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.38e-02 5.25e+03 1.36e+01 bond pdb=" CA SER D 182 " pdb=" CB SER D 182 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.38e-02 5.25e+03 1.33e+01 bond pdb=" CB VAL A 129 " pdb=" CG1 VAL A 129 " ideal model delta sigma weight residual 1.521 1.409 0.112 3.30e-02 9.18e+02 1.14e+01 bond pdb=" CB VAL C 129 " pdb=" CG1 VAL C 129 " ideal model delta sigma weight residual 1.521 1.410 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" CA LEU D 80 " pdb=" C LEU D 80 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.37e-02 5.33e+03 9.02e+00 ... (remaining 16075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 20275 2.02 - 4.03: 1339 4.03 - 6.04: 178 6.04 - 8.06: 60 8.06 - 10.07: 14 Bond angle restraints: 21866 Sorted by residual: angle pdb=" C GLY K 427 " pdb=" N ALA K 428 " pdb=" CA ALA K 428 " ideal model delta sigma weight residual 122.85 115.35 7.50 1.10e+00 8.26e-01 4.64e+01 angle pdb=" C GLY L 427 " pdb=" N ALA L 428 " pdb=" CA ALA L 428 " ideal model delta sigma weight residual 122.85 115.38 7.47 1.10e+00 8.26e-01 4.62e+01 angle pdb=" C VAL C 129 " pdb=" CA VAL C 129 " pdb=" CB VAL C 129 " ideal model delta sigma weight residual 111.29 101.22 10.07 1.64e+00 3.72e-01 3.77e+01 angle pdb=" C VAL A 129 " pdb=" CA VAL A 129 " pdb=" CB VAL A 129 " ideal model delta sigma weight residual 111.29 101.23 10.06 1.64e+00 3.72e-01 3.77e+01 angle pdb=" N SER B 79 " pdb=" CA SER B 79 " pdb=" C SER B 79 " ideal model delta sigma weight residual 114.31 106.62 7.69 1.29e+00 6.01e-01 3.55e+01 ... (remaining 21861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 9015 14.33 - 28.67: 545 28.67 - 43.00: 96 43.00 - 57.33: 6 57.33 - 71.66: 10 Dihedral angle restraints: 9672 sinusoidal: 3368 harmonic: 6304 Sorted by residual: dihedral pdb=" CA CYS A 228 " pdb=" C CYS A 228 " pdb=" N LEU A 229 " pdb=" CA LEU A 229 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS C 228 " pdb=" C CYS C 228 " pdb=" N LEU C 229 " pdb=" CA LEU C 229 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ILE C 92 " pdb=" C ILE C 92 " pdb=" N SER C 93 " pdb=" CA SER C 93 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 9669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2305 0.099 - 0.199: 255 0.199 - 0.298: 16 0.298 - 0.397: 2 0.397 - 0.497: 2 Chirality restraints: 2580 Sorted by residual: chirality pdb=" CB ILE C 218 " pdb=" CA ILE C 218 " pdb=" CG1 ILE C 218 " pdb=" CG2 ILE C 218 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CB ILE A 218 " pdb=" CA ILE A 218 " pdb=" CG1 ILE A 218 " pdb=" CG2 ILE A 218 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CB VAL C 34 " pdb=" CA VAL C 34 " pdb=" CG1 VAL C 34 " pdb=" CG2 VAL C 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 2577 not shown) Planarity restraints: 2848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 132 " 0.035 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE D 132 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE D 132 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 132 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 132 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 132 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 132 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 132 " 0.036 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE B 132 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE B 132 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 132 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 132 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 132 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 132 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 94 " 0.022 2.00e-02 2.50e+03 1.78e-02 7.89e+00 pdb=" CG TRP B 94 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 94 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 94 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 94 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 94 " 0.005 2.00e-02 2.50e+03 ... (remaining 2845 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 171 2.63 - 3.20: 13777 3.20 - 3.76: 22815 3.76 - 4.33: 30871 4.33 - 4.90: 50944 Nonbonded interactions: 118578 Sorted by model distance: nonbonded pdb=" OD2 ASP A 135 " pdb="ZN ZN A 401 " model vdw 2.059 2.230 nonbonded pdb=" OD1 ASP C 135 " pdb="ZN ZN C 401 " model vdw 2.091 2.230 nonbonded pdb=" OD1 ASP A 135 " pdb="ZN ZN A 401 " model vdw 2.097 2.230 nonbonded pdb=" OD2 ASP C 135 " pdb="ZN ZN C 401 " model vdw 2.102 2.230 nonbonded pdb=" OD1 ASN L 78 " pdb=" OG SER L 433 " model vdw 2.298 3.040 ... (remaining 118573 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 4.060 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.013 0.215 16084 Z= 0.560 Angle : 1.145 10.075 21866 Z= 0.643 Chirality : 0.065 0.497 2580 Planarity : 0.008 0.064 2848 Dihedral : 10.253 71.665 5544 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.94 (0.13), residues: 1940 helix: -4.50 (0.08), residues: 840 sheet: -2.98 (0.29), residues: 292 loop : -3.47 (0.17), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 108 TYR 0.040 0.003 TYR A 170 PHE 0.061 0.005 PHE D 132 TRP 0.046 0.005 TRP B 94 HIS 0.016 0.003 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.01269 (16080) covalent geometry : angle 1.14503 (21866) hydrogen bonds : bond 0.30054 ( 597) hydrogen bonds : angle 10.85168 ( 1713) metal coordination : bond 0.18657 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8567 (tmm) cc_final: 0.7789 (ttp) REVERT: A 158 ILE cc_start: 0.9211 (mm) cc_final: 0.8888 (mt) REVERT: A 295 GLN cc_start: 0.7815 (mt0) cc_final: 0.7527 (tm-30) REVERT: B 53 VAL cc_start: 0.8707 (t) cc_final: 0.8231 (m) REVERT: B 228 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7983 (tm-30) REVERT: K 128 ASP cc_start: 0.8024 (t0) cc_final: 0.7767 (t0) REVERT: K 200 LYS cc_start: 0.8454 (ptpt) cc_final: 0.8238 (ptpp) REVERT: K 343 CYS cc_start: 0.7972 (m) cc_final: 0.7172 (t) REVERT: K 346 MET cc_start: 0.8439 (tpp) cc_final: 0.8170 (tpp) REVERT: K 381 LEU cc_start: 0.9437 (pp) cc_final: 0.9193 (pt) REVERT: K 403 VAL cc_start: 0.9410 (m) cc_final: 0.9131 (p) REVERT: C 10 GLN cc_start: 0.8485 (mm110) cc_final: 0.8266 (mt0) REVERT: D 83 ILE cc_start: 0.8417 (mm) cc_final: 0.7569 (mm) REVERT: L 80 CYS cc_start: 0.8066 (m) cc_final: 0.7815 (m) REVERT: L 222 ILE cc_start: 0.8696 (pt) cc_final: 0.8419 (pt) REVERT: L 255 ILE cc_start: 0.9098 (mt) cc_final: 0.8759 (pt) REVERT: E 11 SER cc_start: 0.9318 (t) cc_final: 0.8703 (p) REVERT: E 41 LYS cc_start: 0.8667 (mttt) cc_final: 0.8360 (mmtt) REVERT: E 119 GLU cc_start: 0.7328 (tp30) cc_final: 0.7121 (tp30) REVERT: G 105 TRP cc_start: 0.7809 (t60) cc_final: 0.7181 (t60) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.1465 time to fit residues: 82.8514 Evaluate side-chains 237 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 75 HIS ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 214 ASN K 93 ASN K 254 HIS K 328 HIS K 408 ASN C 75 HIS C 241 GLN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 141 HIS L 270 HIS L 408 ASN E 100 GLN E 125 HIS G 24 ASN G 52 ASN G 125 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112223 restraints weight = 25609.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111706 restraints weight = 19858.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113076 restraints weight = 20881.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113695 restraints weight = 13488.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114019 restraints weight = 12304.270| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16084 Z= 0.149 Angle : 0.626 7.525 21866 Z= 0.330 Chirality : 0.044 0.198 2580 Planarity : 0.005 0.054 2848 Dihedral : 5.633 27.008 2286 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.34 % Allowed : 9.75 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.16), residues: 1940 helix: -2.47 (0.14), residues: 850 sheet: -2.23 (0.28), residues: 324 loop : -3.12 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.019 0.002 TYR A 170 PHE 0.018 0.002 PHE D 132 TRP 0.017 0.002 TRP B 94 HIS 0.010 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00332 (16080) covalent geometry : angle 0.62574 (21866) hydrogen bonds : bond 0.03715 ( 597) hydrogen bonds : angle 5.66625 ( 1713) metal coordination : bond 0.01262 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 329 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8404 (tmm) cc_final: 0.7875 (ttp) REVERT: A 158 ILE cc_start: 0.8832 (mm) cc_final: 0.8484 (mt) REVERT: A 213 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: B 56 ILE cc_start: 0.7743 (mt) cc_final: 0.7506 (mt) REVERT: B 135 THR cc_start: 0.9456 (p) cc_final: 0.9019 (m) REVERT: K 128 ASP cc_start: 0.7970 (t0) cc_final: 0.7714 (t0) REVERT: K 200 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8252 (ptpp) REVERT: K 237 MET cc_start: 0.8029 (mtm) cc_final: 0.7671 (mtm) REVERT: K 343 CYS cc_start: 0.8010 (m) cc_final: 0.7052 (t) REVERT: K 382 VAL cc_start: 0.9477 (OUTLIER) cc_final: 0.9137 (m) REVERT: K 383 LEU cc_start: 0.9236 (tp) cc_final: 0.9010 (mt) REVERT: C 115 MET cc_start: 0.8119 (mmm) cc_final: 0.7683 (mmt) REVERT: C 226 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8315 (ttmt) REVERT: D 16 HIS cc_start: 0.7779 (t-90) cc_final: 0.7491 (t-90) REVERT: D 24 HIS cc_start: 0.7621 (t70) cc_final: 0.7177 (t70) REVERT: L 80 CYS cc_start: 0.7937 (m) cc_final: 0.7630 (m) REVERT: G 35 LEU cc_start: 0.7959 (mm) cc_final: 0.7716 (mp) REVERT: G 54 ASP cc_start: 0.7830 (p0) cc_final: 0.7388 (p0) REVERT: G 77 TYR cc_start: 0.7998 (m-10) cc_final: 0.7717 (m-80) REVERT: G 85 ILE cc_start: 0.8292 (pt) cc_final: 0.8026 (pt) outliers start: 35 outliers final: 17 residues processed: 352 average time/residue: 0.1315 time to fit residues: 67.3718 Evaluate side-chains 260 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 243 GLU Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 406 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 433 SER Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain G residue 72 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 122 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 203 optimal weight: 0.0970 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 293 GLN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 138 ASN B 141 HIS K 328 HIS C 10 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 138 ASN L 408 ASN E 101 ASN G 52 ASN G 74 ASN G 101 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113064 restraints weight = 25703.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112641 restraints weight = 20534.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114132 restraints weight = 18391.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114697 restraints weight = 13267.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114942 restraints weight = 12729.767| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16084 Z= 0.116 Angle : 0.561 8.093 21866 Z= 0.294 Chirality : 0.043 0.266 2580 Planarity : 0.005 0.050 2848 Dihedral : 4.959 24.144 2286 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.94 % Allowed : 14.02 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.18), residues: 1940 helix: -1.27 (0.17), residues: 838 sheet: -1.87 (0.29), residues: 328 loop : -2.75 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 23 TYR 0.017 0.001 TYR C 170 PHE 0.015 0.002 PHE D 132 TRP 0.011 0.001 TRP L 43 HIS 0.009 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00265 (16080) covalent geometry : angle 0.56136 (21866) hydrogen bonds : bond 0.02946 ( 597) hydrogen bonds : angle 4.99702 ( 1713) metal coordination : bond 0.00246 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8253 (tmm) cc_final: 0.7765 (ttp) REVERT: A 158 ILE cc_start: 0.8801 (mm) cc_final: 0.8541 (mt) REVERT: A 213 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: B 228 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7692 (tm-30) REVERT: K 128 ASP cc_start: 0.8022 (t0) cc_final: 0.7740 (t0) REVERT: K 200 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8230 (ptpp) REVERT: K 343 CYS cc_start: 0.7910 (m) cc_final: 0.6974 (t) REVERT: K 382 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.8969 (m) REVERT: K 383 LEU cc_start: 0.9243 (tp) cc_final: 0.8971 (mt) REVERT: C 115 MET cc_start: 0.8051 (mmm) cc_final: 0.7735 (mmm) REVERT: C 226 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8228 (ttpt) REVERT: C 289 ASP cc_start: 0.7450 (t70) cc_final: 0.7072 (t0) REVERT: D 31 GLU cc_start: 0.7942 (pp20) cc_final: 0.7683 (pp20) REVERT: D 231 GLU cc_start: 0.6936 (tt0) cc_final: 0.6692 (tt0) REVERT: L 80 CYS cc_start: 0.7731 (m) cc_final: 0.7509 (m) REVERT: L 228 TYR cc_start: 0.8247 (t80) cc_final: 0.8037 (t80) REVERT: E 52 ASN cc_start: 0.7721 (p0) cc_final: 0.7299 (p0) REVERT: E 77 TYR cc_start: 0.7209 (m-80) cc_final: 0.6885 (m-80) REVERT: E 101 ASN cc_start: 0.8136 (m-40) cc_final: 0.7813 (m110) REVERT: E 118 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8656 (mttm) REVERT: E 119 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6253 (mt-10) REVERT: G 7 LEU cc_start: 0.7548 (mt) cc_final: 0.7045 (tt) REVERT: G 54 ASP cc_start: 0.7560 (p0) cc_final: 0.7153 (p0) outliers start: 44 outliers final: 23 residues processed: 307 average time/residue: 0.1293 time to fit residues: 58.0041 Evaluate side-chains 266 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 433 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 172 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 166 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 210 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN E 59 HIS G 24 ASN G 52 ASN G 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109641 restraints weight = 25770.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108747 restraints weight = 20762.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110183 restraints weight = 20447.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110712 restraints weight = 14307.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111015 restraints weight = 13175.171| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16084 Z= 0.159 Angle : 0.586 8.444 21866 Z= 0.302 Chirality : 0.044 0.182 2580 Planarity : 0.004 0.040 2848 Dihedral : 4.854 23.561 2286 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.94 % Allowed : 14.82 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.19), residues: 1940 helix: -0.61 (0.18), residues: 842 sheet: -1.98 (0.28), residues: 334 loop : -2.65 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 81 TYR 0.015 0.002 TYR A 170 PHE 0.028 0.002 PHE D 132 TRP 0.010 0.001 TRP G 105 HIS 0.010 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00372 (16080) covalent geometry : angle 0.58618 (21866) hydrogen bonds : bond 0.02901 ( 597) hydrogen bonds : angle 4.82180 ( 1713) metal coordination : bond 0.00563 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8294 (tmm) cc_final: 0.7679 (ttp) REVERT: B 144 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: B 229 LYS cc_start: 0.8493 (mttt) cc_final: 0.8275 (mtmm) REVERT: K 128 ASP cc_start: 0.8016 (t0) cc_final: 0.7654 (t0) REVERT: K 343 CYS cc_start: 0.7890 (m) cc_final: 0.7019 (t) REVERT: K 382 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.8954 (m) REVERT: K 383 LEU cc_start: 0.9209 (tp) cc_final: 0.8964 (mt) REVERT: C 289 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7241 (t70) REVERT: D 64 LYS cc_start: 0.6755 (mttp) cc_final: 0.6138 (mmmt) REVERT: D 231 GLU cc_start: 0.7028 (tt0) cc_final: 0.6763 (tt0) REVERT: L 228 TYR cc_start: 0.8318 (t80) cc_final: 0.8078 (t80) REVERT: E 118 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8590 (mttp) REVERT: E 119 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6309 (mt-10) REVERT: G 7 LEU cc_start: 0.7483 (mt) cc_final: 0.7033 (tt) REVERT: G 54 ASP cc_start: 0.7336 (p0) cc_final: 0.7130 (p0) REVERT: G 105 TRP cc_start: 0.8207 (t60) cc_final: 0.7610 (t60) outliers start: 59 outliers final: 31 residues processed: 295 average time/residue: 0.1285 time to fit residues: 55.9302 Evaluate side-chains 267 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 433 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 157 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 208 optimal weight: 30.0000 chunk 182 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN K 279 HIS K 328 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN G 52 ASN G 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109369 restraints weight = 25928.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108503 restraints weight = 20833.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109936 restraints weight = 20452.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110469 restraints weight = 14298.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110834 restraints weight = 13278.748| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16084 Z= 0.148 Angle : 0.566 9.043 21866 Z= 0.292 Chirality : 0.043 0.177 2580 Planarity : 0.004 0.053 2848 Dihedral : 4.678 23.031 2286 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.74 % Allowed : 16.89 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.19), residues: 1940 helix: -0.26 (0.18), residues: 846 sheet: -1.97 (0.30), residues: 282 loop : -2.49 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 33 TYR 0.015 0.001 TYR A 170 PHE 0.025 0.002 PHE D 132 TRP 0.009 0.001 TRP D 94 HIS 0.009 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00346 (16080) covalent geometry : angle 0.56616 (21866) hydrogen bonds : bond 0.02698 ( 597) hydrogen bonds : angle 4.66891 ( 1713) metal coordination : bond 0.00498 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8241 (tmm) cc_final: 0.7848 (ptm) REVERT: B 53 VAL cc_start: 0.8413 (t) cc_final: 0.8069 (m) REVERT: B 229 LYS cc_start: 0.8502 (mttt) cc_final: 0.8248 (mtmm) REVERT: K 128 ASP cc_start: 0.7995 (t0) cc_final: 0.7642 (t0) REVERT: K 343 CYS cc_start: 0.7835 (m) cc_final: 0.6980 (t) REVERT: K 382 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8878 (m) REVERT: D 64 LYS cc_start: 0.6699 (mttp) cc_final: 0.6199 (mmmt) REVERT: D 231 GLU cc_start: 0.7260 (tt0) cc_final: 0.6907 (tt0) REVERT: L 228 TYR cc_start: 0.8348 (t80) cc_final: 0.8113 (t80) REVERT: L 292 TYR cc_start: 0.9174 (p90) cc_final: 0.8926 (p90) REVERT: L 371 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7772 (p) REVERT: E 52 ASN cc_start: 0.7855 (p0) cc_final: 0.7616 (p0) REVERT: E 55 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8231 (mtt90) REVERT: E 118 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8506 (mttp) REVERT: G 7 LEU cc_start: 0.7473 (mt) cc_final: 0.7010 (tt) REVERT: G 105 TRP cc_start: 0.8255 (t60) cc_final: 0.7514 (t60) outliers start: 56 outliers final: 41 residues processed: 284 average time/residue: 0.1238 time to fit residues: 52.0822 Evaluate side-chains 276 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 346 MET Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 433 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 131 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 204 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN G 52 ASN G 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108733 restraints weight = 25993.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107896 restraints weight = 20637.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109396 restraints weight = 20904.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109878 restraints weight = 14513.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110224 restraints weight = 13277.015| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16084 Z= 0.143 Angle : 0.558 7.651 21866 Z= 0.288 Chirality : 0.043 0.191 2580 Planarity : 0.004 0.039 2848 Dihedral : 4.567 23.081 2286 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.21 % Allowed : 16.42 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.19), residues: 1940 helix: 0.05 (0.19), residues: 844 sheet: -1.83 (0.32), residues: 272 loop : -2.43 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 23 TYR 0.020 0.001 TYR L 195 PHE 0.022 0.001 PHE D 132 TRP 0.007 0.001 TRP D 94 HIS 0.009 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00333 (16080) covalent geometry : angle 0.55829 (21866) hydrogen bonds : bond 0.02659 ( 597) hydrogen bonds : angle 4.53863 ( 1713) metal coordination : bond 0.00494 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 244 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8356 (mp10) cc_final: 0.7750 (mp10) REVERT: A 35 MET cc_start: 0.8138 (tmm) cc_final: 0.7804 (ptm) REVERT: B 53 VAL cc_start: 0.8411 (t) cc_final: 0.8070 (m) REVERT: B 143 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8141 (tt) REVERT: B 229 LYS cc_start: 0.8423 (mttt) cc_final: 0.8221 (mtmm) REVERT: K 128 ASP cc_start: 0.8014 (t0) cc_final: 0.7658 (t0) REVERT: K 343 CYS cc_start: 0.7877 (m) cc_final: 0.7052 (t) REVERT: K 382 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8864 (m) REVERT: D 64 LYS cc_start: 0.6584 (mttp) cc_final: 0.6103 (mmmt) REVERT: D 231 GLU cc_start: 0.7302 (tt0) cc_final: 0.7016 (tt0) REVERT: L 228 TYR cc_start: 0.8379 (t80) cc_final: 0.8171 (t80) REVERT: L 292 TYR cc_start: 0.9142 (p90) cc_final: 0.8908 (p90) REVERT: L 371 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7745 (p) REVERT: G 7 LEU cc_start: 0.7518 (mt) cc_final: 0.7005 (tt) REVERT: G 101 ASN cc_start: 0.7155 (t160) cc_final: 0.6175 (t0) REVERT: G 105 TRP cc_start: 0.8217 (t60) cc_final: 0.7412 (t60) outliers start: 63 outliers final: 45 residues processed: 285 average time/residue: 0.1273 time to fit residues: 53.6769 Evaluate side-chains 283 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 406 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain L residue 68 CYS Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 346 MET Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 433 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 15 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 211 optimal weight: 30.0000 chunk 54 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 204 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 192 HIS L 408 ASN G 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108216 restraints weight = 26151.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107598 restraints weight = 20565.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108876 restraints weight = 19607.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109399 restraints weight = 14245.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109624 restraints weight = 13342.096| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16084 Z= 0.128 Angle : 0.556 10.402 21866 Z= 0.285 Chirality : 0.042 0.181 2580 Planarity : 0.004 0.043 2848 Dihedral : 4.440 23.171 2286 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.41 % Allowed : 17.36 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.19), residues: 1940 helix: 0.20 (0.19), residues: 854 sheet: -1.84 (0.32), residues: 262 loop : -2.35 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 23 TYR 0.014 0.001 TYR A 170 PHE 0.020 0.001 PHE D 132 TRP 0.006 0.001 TRP D 94 HIS 0.007 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00299 (16080) covalent geometry : angle 0.55636 (21866) hydrogen bonds : bond 0.02582 ( 597) hydrogen bonds : angle 4.43079 ( 1713) metal coordination : bond 0.00412 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8322 (mp10) cc_final: 0.7586 (mp10) REVERT: A 35 MET cc_start: 0.8161 (tmm) cc_final: 0.7554 (ptt) REVERT: B 53 VAL cc_start: 0.8405 (t) cc_final: 0.8063 (m) REVERT: B 229 LYS cc_start: 0.8448 (mttt) cc_final: 0.8147 (mtmm) REVERT: K 128 ASP cc_start: 0.8017 (t0) cc_final: 0.7714 (t0) REVERT: K 237 MET cc_start: 0.8138 (mtt) cc_final: 0.7923 (mtt) REVERT: K 343 CYS cc_start: 0.7883 (m) cc_final: 0.7079 (t) REVERT: K 382 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8811 (m) REVERT: C 17 ASP cc_start: 0.7649 (p0) cc_final: 0.7002 (p0) REVERT: C 105 GLU cc_start: 0.8308 (tp30) cc_final: 0.8093 (mm-30) REVERT: D 64 LYS cc_start: 0.6529 (mttp) cc_final: 0.6061 (mmmt) REVERT: L 43 TRP cc_start: 0.6408 (m-90) cc_final: 0.6042 (m-10) REVERT: L 292 TYR cc_start: 0.9101 (p90) cc_final: 0.8865 (p90) REVERT: L 371 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7746 (p) REVERT: L 381 LEU cc_start: 0.9159 (pp) cc_final: 0.8936 (pp) REVERT: E 118 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8493 (mttp) REVERT: G 101 ASN cc_start: 0.7318 (t160) cc_final: 0.6914 (t0) REVERT: G 105 TRP cc_start: 0.8254 (t60) cc_final: 0.7475 (t60) outliers start: 66 outliers final: 48 residues processed: 290 average time/residue: 0.1346 time to fit residues: 57.7388 Evaluate side-chains 285 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 406 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 346 MET Chi-restraints excluded: chain L residue 371 SER Chi-restraints excluded: chain L residue 433 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 140 optimal weight: 0.0000 chunk 32 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 95 optimal weight: 0.0870 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN L 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110366 restraints weight = 26328.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109118 restraints weight = 21211.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110796 restraints weight = 19986.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111186 restraints weight = 13977.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111512 restraints weight = 13361.430| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16084 Z= 0.108 Angle : 0.551 10.092 21866 Z= 0.281 Chirality : 0.041 0.163 2580 Planarity : 0.004 0.045 2848 Dihedral : 4.260 22.133 2286 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.01 % Allowed : 18.02 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1940 helix: 0.53 (0.19), residues: 852 sheet: -1.68 (0.33), residues: 262 loop : -2.32 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 23 TYR 0.019 0.001 TYR L 195 PHE 0.018 0.001 PHE D 132 TRP 0.006 0.001 TRP D 94 HIS 0.006 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00249 (16080) covalent geometry : angle 0.55145 (21866) hydrogen bonds : bond 0.02419 ( 597) hydrogen bonds : angle 4.31764 ( 1713) metal coordination : bond 0.00242 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 252 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8119 (tmm) cc_final: 0.7601 (ptt) REVERT: A 81 ARG cc_start: 0.8239 (ptm-80) cc_final: 0.7927 (ptm-80) REVERT: B 229 LYS cc_start: 0.8397 (mttt) cc_final: 0.8158 (mtmm) REVERT: K 128 ASP cc_start: 0.7989 (t0) cc_final: 0.7613 (t0) REVERT: K 343 CYS cc_start: 0.7795 (m) cc_final: 0.7011 (t) REVERT: K 382 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8714 (m) REVERT: C 14 LEU cc_start: 0.8194 (tp) cc_final: 0.7738 (tp) REVERT: C 17 ASP cc_start: 0.7551 (p0) cc_final: 0.6827 (p0) REVERT: C 105 GLU cc_start: 0.8292 (tp30) cc_final: 0.8072 (mm-30) REVERT: D 64 LYS cc_start: 0.6461 (mttp) cc_final: 0.6060 (mmmt) REVERT: L 292 TYR cc_start: 0.9106 (p90) cc_final: 0.8904 (p90) REVERT: E 52 ASN cc_start: 0.7699 (p0) cc_final: 0.7197 (p0) REVERT: E 118 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8493 (mttp) outliers start: 60 outliers final: 45 residues processed: 289 average time/residue: 0.1370 time to fit residues: 58.4654 Evaluate side-chains 283 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 433 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 203 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 40 optimal weight: 0.0770 chunk 172 optimal weight: 0.0370 chunk 55 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 136 optimal weight: 0.0770 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** K 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN C 299 GLN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN G 101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111748 restraints weight = 25975.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112370 restraints weight = 20154.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113542 restraints weight = 18097.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113993 restraints weight = 13522.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114235 restraints weight = 12513.711| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16084 Z= 0.098 Angle : 0.559 9.705 21866 Z= 0.281 Chirality : 0.041 0.153 2580 Planarity : 0.004 0.052 2848 Dihedral : 4.087 22.381 2286 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.07 % Allowed : 19.09 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.20), residues: 1940 helix: 0.83 (0.19), residues: 836 sheet: -1.48 (0.34), residues: 252 loop : -2.26 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 62 TYR 0.017 0.001 TYR L 195 PHE 0.016 0.001 PHE D 132 TRP 0.005 0.001 TRP C 130 HIS 0.005 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00225 (16080) covalent geometry : angle 0.55855 (21866) hydrogen bonds : bond 0.02343 ( 597) hydrogen bonds : angle 4.19406 ( 1713) metal coordination : bond 0.00130 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 256 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 THR cc_start: 0.9229 (p) cc_final: 0.9014 (m) REVERT: B 229 LYS cc_start: 0.8298 (mttt) cc_final: 0.8091 (mtmm) REVERT: K 128 ASP cc_start: 0.8015 (t0) cc_final: 0.7610 (t0) REVERT: K 381 LEU cc_start: 0.9150 (pt) cc_final: 0.8761 (pp) REVERT: K 382 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8622 (m) REVERT: K 431 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7481 (mm) REVERT: C 14 LEU cc_start: 0.8070 (tp) cc_final: 0.7524 (tp) REVERT: C 17 ASP cc_start: 0.7583 (p0) cc_final: 0.6860 (p0) REVERT: C 115 MET cc_start: 0.7820 (mmm) cc_final: 0.7501 (mmm) REVERT: C 226 LYS cc_start: 0.8499 (tppp) cc_final: 0.8271 (tppt) REVERT: D 64 LYS cc_start: 0.6581 (mttp) cc_final: 0.6206 (mmmt) outliers start: 46 outliers final: 37 residues processed: 283 average time/residue: 0.1280 time to fit residues: 53.8858 Evaluate side-chains 280 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 431 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 70 optimal weight: 0.0870 chunk 153 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 140 optimal weight: 0.0770 chunk 98 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 408 ASN ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111394 restraints weight = 25764.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111361 restraints weight = 20025.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112360 restraints weight = 19583.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113074 restraints weight = 14456.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113318 restraints weight = 12698.343| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16084 Z= 0.113 Angle : 0.574 9.997 21866 Z= 0.289 Chirality : 0.042 0.157 2580 Planarity : 0.004 0.061 2848 Dihedral : 4.104 22.776 2286 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.87 % Allowed : 19.83 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1940 helix: 0.84 (0.19), residues: 848 sheet: -1.38 (0.34), residues: 252 loop : -2.21 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 62 TYR 0.019 0.001 TYR L 195 PHE 0.017 0.001 PHE D 132 TRP 0.006 0.001 TRP L 134 HIS 0.006 0.001 HIS D 16 Details of bonding type rmsd covalent geometry : bond 0.00263 (16080) covalent geometry : angle 0.57402 (21866) hydrogen bonds : bond 0.02394 ( 597) hydrogen bonds : angle 4.20146 ( 1713) metal coordination : bond 0.00305 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 128 ASP cc_start: 0.8037 (t0) cc_final: 0.7644 (t0) REVERT: K 343 CYS cc_start: 0.7715 (m) cc_final: 0.7069 (t) REVERT: K 382 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8673 (m) REVERT: K 431 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7525 (mm) REVERT: C 14 LEU cc_start: 0.8157 (tp) cc_final: 0.7664 (tp) REVERT: C 17 ASP cc_start: 0.7641 (p0) cc_final: 0.6935 (p0) REVERT: C 115 MET cc_start: 0.7787 (mmm) cc_final: 0.7484 (mmm) REVERT: C 226 LYS cc_start: 0.8621 (tppp) cc_final: 0.8371 (tppt) REVERT: D 64 LYS cc_start: 0.6549 (mttp) cc_final: 0.6163 (mmmt) REVERT: E 118 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8537 (mttp) outliers start: 43 outliers final: 38 residues processed: 277 average time/residue: 0.1332 time to fit residues: 54.7569 Evaluate side-chains 284 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 276 THR Chi-restraints excluded: chain K residue 382 VAL Chi-restraints excluded: chain K residue 431 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain G residue 71 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 210 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 202 optimal weight: 3.9990 chunk 77 optimal weight: 0.0270 chunk 97 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 chunk 174 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN ** D 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 GLN L 408 ASN ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113593 restraints weight = 25538.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113746 restraints weight = 19816.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114988 restraints weight = 17903.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115486 restraints weight = 13308.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115748 restraints weight = 12017.255| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16084 Z= 0.098 Angle : 0.562 9.859 21866 Z= 0.281 Chirality : 0.041 0.207 2580 Planarity : 0.004 0.054 2848 Dihedral : 3.965 21.910 2286 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.87 % Allowed : 20.43 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.20), residues: 1940 helix: 0.97 (0.19), residues: 852 sheet: -1.27 (0.34), residues: 252 loop : -2.21 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 62 TYR 0.021 0.001 TYR L 195 PHE 0.018 0.001 PHE C 173 TRP 0.008 0.001 TRP L 43 HIS 0.007 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00228 (16080) covalent geometry : angle 0.56230 (21866) hydrogen bonds : bond 0.02273 ( 597) hydrogen bonds : angle 4.10702 ( 1713) metal coordination : bond 0.00142 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.03 seconds wall clock time: 43 minutes 21.47 seconds (2601.47 seconds total)