Starting phenix.real_space_refine on Thu Feb 5 03:00:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dfs_46818/02_2026/9dfs_46818.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dfs_46818/02_2026/9dfs_46818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dfs_46818/02_2026/9dfs_46818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dfs_46818/02_2026/9dfs_46818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dfs_46818/02_2026/9dfs_46818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dfs_46818/02_2026/9dfs_46818.map" } resolution = 3.1 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= 0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 97 5.16 5 C 9037 2.51 5 N 2443 2.21 5 O 2717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14306 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2893 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2911 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2951 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 5490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5490 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 27, 'TRANS': 653} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AVAL B 45 " occ=0.48 ... (12 atoms not shown) pdb=" CG2BVAL B 45 " occ=0.52 residue: pdb=" N AGLY B 46 " occ=0.48 ... (6 atoms not shown) pdb=" O BGLY B 46 " occ=0.52 Time building chain proxies: 3.35, per 1000 atoms: 0.23 Number of scatterers: 14306 At special positions: 0 Unit cell: (91.8, 154.44, 139.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 97 16.00 P 8 15.00 Mg 4 11.99 O 2717 8.00 N 2443 7.00 C 9037 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: 1.05 Conformation dependent library (CDL) restraints added in 631.5 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 24 sheets defined 49.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.781A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.833A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.549A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.555A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.640A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.540A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.854A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.578A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.565A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.531A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.814A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.247A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.523A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.614A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 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 202 through 217 removed outlier: 3.923A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.571A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.647A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.815A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.091A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.733A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.870A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.585A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.552A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.549A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.159A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.632A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.854A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.521A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.525A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.877A pdb=" N HIS D 97 " --> pdb=" O PRO D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 165 through 181 removed outlier: 3.700A pdb=" N ILE D 169 " --> pdb=" O HIS D 165 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET D 177 " --> pdb=" O CYS D 173 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 178 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 212 removed outlier: 3.784A pdb=" N PHE D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 207 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 232 removed outlier: 3.561A pdb=" N GLU D 218 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Proline residue: D 226 - end of helix removed outlier: 3.651A pdb=" N ALA D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 275 removed outlier: 3.536A pdb=" N ARG D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 274 " --> pdb=" O LYS D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 293 removed outlier: 4.411A pdb=" N TYR D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 327 through 340 removed outlier: 3.636A pdb=" N ALA D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'D' and resid 381 through 392 removed outlier: 4.046A pdb=" N ALA D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 403 removed outlier: 3.786A pdb=" N CYS D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 403 " --> pdb=" O MET D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 451 removed outlier: 3.854A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 512 removed outlier: 3.609A pdb=" N HIS D 492 " --> pdb=" O PHE D 488 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU D 512 " --> pdb=" O GLU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.819A pdb=" N LEU D 528 " --> pdb=" O ASN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 548 removed outlier: 3.695A pdb=" N LYS D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 565 Processing helix chain 'D' and resid 606 through 615 removed outlier: 3.781A pdb=" N ILE D 610 " --> pdb=" O HIS D 606 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS D 614 " --> pdb=" O ILE D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.652A pdb=" N LYS D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 631 removed outlier: 3.618A pdb=" N MET D 631 " --> pdb=" O ALA D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 635 removed outlier: 4.032A pdb=" N THR D 635 " --> pdb=" O GLY D 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 632 through 635' Processing helix chain 'D' and resid 641 through 659 removed outlier: 3.774A pdb=" N ALA D 659 " --> pdb=" O ARG D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 691 removed outlier: 3.629A pdb=" N ARG D 686 " --> pdb=" O HIS D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 703 removed outlier: 4.256A pdb=" N ILE D 697 " --> pdb=" O MET D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.705A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.815A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.815A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.510A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.939A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.845A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.524A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 41 through 44 removed outlier: 3.509A pdb=" N VAL D 71 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 69 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 127 through 130 removed outlier: 6.482A pdb=" N CYS D 185 " --> pdb=" O PHE D 663 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL D 665 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE D 187 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N CYS D 667 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER D 189 " --> pdb=" O CYS D 667 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY D 190 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS D 247 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY D 261 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 233 through 234 Processing sheet with id=AC4, first strand: chain 'D' and resid 365 through 369 Processing sheet with id=AC5, first strand: chain 'D' and resid 404 through 409 Processing sheet with id=AC6, first strand: chain 'D' and resid 570 through 571 647 hydrogen bonds defined for protein. 1731 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: 2.24 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2435 1.32 - 1.44: 3808 1.44 - 1.56: 8200 1.56 - 1.69: 12 1.69 - 1.81: 165 Bond restraints: 14620 Sorted by residual: bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.14e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.66e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C GLY C 156 " pdb=" O GLY C 156 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.35e-02 5.49e+03 7.14e+00 bond pdb=" CA GLY A 301 " pdb=" C GLY A 301 " ideal model delta sigma weight residual 1.520 1.495 0.025 1.12e-02 7.97e+03 4.88e+00 ... (remaining 14615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 19404 1.94 - 3.87: 341 3.87 - 5.81: 55 5.81 - 7.74: 16 7.74 - 9.68: 1 Bond angle restraints: 19817 Sorted by residual: angle pdb=" N THR A 304 " pdb=" CA THR A 304 " pdb=" C THR A 304 " ideal model delta sigma weight residual 112.92 106.45 6.47 1.23e+00 6.61e-01 2.76e+01 angle pdb=" N ALA D 308 " pdb=" CA ALA D 308 " pdb=" C ALA D 308 " ideal model delta sigma weight residual 113.17 106.86 6.31 1.26e+00 6.30e-01 2.51e+01 angle pdb=" N THR A 303 " pdb=" CA THR A 303 " pdb=" C THR A 303 " ideal model delta sigma weight residual 113.16 107.06 6.10 1.24e+00 6.50e-01 2.42e+01 angle pdb=" N PRO D 455 " pdb=" CA PRO D 455 " pdb=" C PRO D 455 " ideal model delta sigma weight residual 114.03 108.07 5.96 1.23e+00 6.61e-01 2.35e+01 angle pdb=" N VAL B 152 " pdb=" CA VAL B 152 " pdb=" C VAL B 152 " ideal model delta sigma weight residual 108.36 114.83 -6.47 1.43e+00 4.89e-01 2.05e+01 ... (remaining 19812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 8491 25.98 - 51.97: 284 51.97 - 77.95: 22 77.95 - 103.94: 3 103.94 - 129.92: 4 Dihedral angle restraints: 8804 sinusoidal: 3593 harmonic: 5211 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 69.92 -129.92 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" C5' ADP D1102 " pdb=" O5' ADP D1102 " pdb=" PA ADP D1102 " pdb=" O2A ADP D1102 " ideal model delta sinusoidal sigma weight residual -60.00 49.08 -109.07 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -166.99 106.99 1 2.00e+01 2.50e-03 3.10e+01 ... (remaining 8801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1360 0.034 - 0.068: 584 0.068 - 0.102: 162 0.102 - 0.137: 72 0.137 - 0.171: 3 Chirality restraints: 2181 Sorted by residual: chirality pdb=" CG LEU D 268 " pdb=" CB LEU D 268 " pdb=" CD1 LEU D 268 " pdb=" CD2 LEU D 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA ASP D 510 " pdb=" N ASP D 510 " pdb=" C ASP D 510 " pdb=" CB ASP D 510 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA TYR D 284 " pdb=" N TYR D 284 " pdb=" C TYR D 284 " pdb=" CB TYR D 284 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 2178 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 534 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO D 535 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 535 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 535 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 112 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 97 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO A 98 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.024 5.00e-02 4.00e+02 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 425 2.71 - 3.26: 13737 3.26 - 3.81: 22121 3.81 - 4.35: 30570 4.35 - 4.90: 50493 Nonbonded interactions: 117346 Sorted by model distance: nonbonded pdb=" OG1 THR D 197 " pdb="MG MG D1101 " model vdw 2.167 2.170 nonbonded pdb="MG MG D1101 " pdb=" O2B ADP D1102 " model vdw 2.217 2.170 nonbonded pdb=" OD2 ASP A 211 " pdb=" OH TYR A 240 " model vdw 2.229 3.040 nonbonded pdb=" NZ LYS B 18 " pdb=" O1B ADP B 401 " model vdw 2.231 3.120 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.236 3.040 ... (remaining 117341 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 44 or resid 47 through 402)) selection = (chain 'B' and (resid 6 through 44 or resid 47 through 402)) selection = (chain 'C' and (resid 6 through 44 or resid 47 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.210 Find NCS groups from input model: 0.210 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14620 Z= 0.191 Angle : 0.644 9.680 19817 Z= 0.363 Chirality : 0.043 0.171 2181 Planarity : 0.004 0.053 2550 Dihedral : 12.604 129.925 5458 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.26 % Allowed : 0.39 % Favored : 99.35 % 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: -1.38 (0.20), residues: 1780 helix: -1.03 (0.18), residues: 763 sheet: -0.56 (0.29), residues: 311 loop : -0.69 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 716 TYR 0.012 0.001 TYR D 310 PHE 0.014 0.001 PHE D 167 TRP 0.011 0.001 TRP B 79 HIS 0.005 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00330 (14620) covalent geometry : angle 0.64400 (19817) hydrogen bonds : bond 0.24104 ( 640) hydrogen bonds : angle 7.87929 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 266 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8441 (t80) cc_final: 0.8091 (t80) REVERT: B 80 ASP cc_start: 0.8002 (m-30) cc_final: 0.7771 (m-30) REVERT: B 82 MET cc_start: 0.8332 (tpt) cc_final: 0.8014 (tpt) REVERT: B 121 GLN cc_start: 0.8335 (tt0) cc_final: 0.8134 (tt0) REVERT: B 211 ASP cc_start: 0.7845 (t0) cc_final: 0.7639 (t70) REVERT: B 215 LYS cc_start: 0.8114 (mttt) cc_final: 0.7870 (mtpt) REVERT: C 211 ASP cc_start: 0.7427 (m-30) cc_final: 0.7209 (m-30) REVERT: D 181 ASN cc_start: 0.7104 (m110) cc_final: 0.6657 (t0) REVERT: D 218 GLU cc_start: 0.7632 (tp30) cc_final: 0.7038 (tt0) REVERT: D 366 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7938 (mt-10) REVERT: D 399 MET cc_start: 0.8062 (tpt) cc_final: 0.7578 (tpp) outliers start: 4 outliers final: 2 residues processed: 269 average time/residue: 0.1298 time to fit residues: 49.6957 Evaluate side-chains 201 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 159 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 353 GLN B 225 ASN B 354 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 172 ASN D 614 HIS D 671 ASN D 687 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.154305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114595 restraints weight = 28021.268| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.33 r_work: 0.2787 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14620 Z= 0.179 Angle : 0.642 8.214 19817 Z= 0.323 Chirality : 0.046 0.167 2181 Planarity : 0.005 0.049 2550 Dihedral : 8.519 140.905 2010 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 0.84 % Allowed : 5.32 % Favored : 93.84 % 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: -0.83 (0.20), residues: 1780 helix: -0.47 (0.18), residues: 792 sheet: -0.24 (0.28), residues: 321 loop : -0.56 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 602 TYR 0.014 0.001 TYR C 362 PHE 0.021 0.002 PHE D 167 TRP 0.014 0.002 TRP B 79 HIS 0.007 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00427 (14620) covalent geometry : angle 0.64151 (19817) hydrogen bonds : bond 0.04704 ( 640) hydrogen bonds : angle 5.16615 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 0.572 Fit side-chains REVERT: A 41 GLN cc_start: 0.8767 (tt0) cc_final: 0.8518 (tt0) REVERT: A 166 TYR cc_start: 0.8731 (t80) cc_final: 0.8441 (t80) REVERT: A 360 GLN cc_start: 0.8142 (mp-120) cc_final: 0.7938 (mp10) REVERT: C 211 ASP cc_start: 0.7503 (m-30) cc_final: 0.7262 (m-30) REVERT: C 236 LEU cc_start: 0.8076 (mt) cc_final: 0.7831 (mp) REVERT: D 280 ASP cc_start: 0.8258 (t0) cc_final: 0.7897 (t0) REVERT: D 292 GLU cc_start: 0.8324 (mp0) cc_final: 0.8081 (mp0) REVERT: D 318 CYS cc_start: 0.7853 (m) cc_final: 0.7574 (m) REVERT: D 366 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8120 (mt-10) REVERT: D 575 ASN cc_start: 0.8555 (m110) cc_final: 0.8352 (m-40) outliers start: 13 outliers final: 6 residues processed: 224 average time/residue: 0.1295 time to fit residues: 41.8674 Evaluate side-chains 198 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 619 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 77 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 225 ASN C 101 HIS D 614 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.154892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.117040 restraints weight = 35697.341| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.56 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14620 Z= 0.173 Angle : 0.613 7.399 19817 Z= 0.306 Chirality : 0.045 0.156 2181 Planarity : 0.005 0.054 2550 Dihedral : 8.453 138.463 2008 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.10 % Allowed : 7.85 % Favored : 91.04 % 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: -0.47 (0.20), residues: 1780 helix: -0.06 (0.19), residues: 788 sheet: -0.05 (0.29), residues: 319 loop : -0.53 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 179 TYR 0.015 0.001 TYR D 310 PHE 0.017 0.002 PHE D 342 TRP 0.016 0.002 TRP B 79 HIS 0.006 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00416 (14620) covalent geometry : angle 0.61304 (19817) hydrogen bonds : bond 0.04322 ( 640) hydrogen bonds : angle 4.87378 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8686 (t80) cc_final: 0.8272 (t80) REVERT: A 167 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7786 (tp30) REVERT: B 28 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7735 (ttm-80) REVERT: B 82 MET cc_start: 0.8523 (tpt) cc_final: 0.8284 (tpt) REVERT: B 176 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8098 (mtp) REVERT: C 206 ARG cc_start: 0.7475 (ttm170) cc_final: 0.7228 (ttm-80) REVERT: D 238 ARG cc_start: 0.7885 (mmt90) cc_final: 0.7565 (mtt90) REVERT: D 280 ASP cc_start: 0.7832 (t0) cc_final: 0.7426 (t0) REVERT: D 366 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7930 (mp0) REVERT: D 507 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: D 575 ASN cc_start: 0.8481 (m110) cc_final: 0.8263 (m-40) outliers start: 17 outliers final: 10 residues processed: 209 average time/residue: 0.1312 time to fit residues: 39.3990 Evaluate side-chains 203 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 605 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 117 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 353 GLN B 225 ASN D 614 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.153797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.114973 restraints weight = 38455.479| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 5.27 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14620 Z= 0.128 Angle : 0.567 7.235 19817 Z= 0.280 Chirality : 0.044 0.145 2181 Planarity : 0.004 0.055 2550 Dihedral : 8.293 138.033 2008 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.97 % Allowed : 9.21 % Favored : 89.81 % 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: -0.13 (0.20), residues: 1780 helix: 0.27 (0.19), residues: 789 sheet: 0.06 (0.28), residues: 327 loop : -0.40 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 602 TYR 0.012 0.001 TYR D 310 PHE 0.014 0.001 PHE D 342 TRP 0.014 0.001 TRP B 79 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00298 (14620) covalent geometry : angle 0.56700 (19817) hydrogen bonds : bond 0.03517 ( 640) hydrogen bonds : angle 4.64307 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8121 (t0) cc_final: 0.7889 (t0) REVERT: A 167 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7839 (tp30) REVERT: B 28 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7841 (ttm-80) REVERT: B 176 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7816 (mtp) REVERT: C 206 ARG cc_start: 0.7338 (ttm170) cc_final: 0.7055 (ttm-80) REVERT: D 158 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7437 (mtpp) REVERT: D 366 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7858 (mp0) REVERT: D 575 ASN cc_start: 0.8362 (m110) cc_final: 0.8130 (m-40) REVERT: D 599 GLU cc_start: 0.7556 (tt0) cc_final: 0.7141 (tt0) outliers start: 15 outliers final: 11 residues processed: 205 average time/residue: 0.1353 time to fit residues: 39.0738 Evaluate side-chains 204 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 699 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 107 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 144 optimal weight: 0.4980 chunk 142 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 225 ASN D 490 ASN D 614 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.152682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.114025 restraints weight = 21644.164| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.45 r_work: 0.2854 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14620 Z= 0.135 Angle : 0.570 7.215 19817 Z= 0.280 Chirality : 0.044 0.148 2181 Planarity : 0.004 0.053 2550 Dihedral : 8.212 138.160 2008 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.36 % Allowed : 9.67 % Favored : 88.97 % 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: 0.06 (0.20), residues: 1780 helix: 0.44 (0.19), residues: 788 sheet: 0.12 (0.28), residues: 327 loop : -0.30 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 372 TYR 0.013 0.001 TYR D 310 PHE 0.014 0.001 PHE D 342 TRP 0.013 0.001 TRP B 79 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00323 (14620) covalent geometry : angle 0.56995 (19817) hydrogen bonds : bond 0.03458 ( 640) hydrogen bonds : angle 4.56438 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.391 Fit side-chains REVERT: A 72 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: A 166 TYR cc_start: 0.8664 (t80) cc_final: 0.8408 (t80) REVERT: A 167 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7997 (tp30) REVERT: B 28 ARG cc_start: 0.8787 (ttm170) cc_final: 0.8516 (ttm-80) REVERT: B 176 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8669 (mtp) REVERT: C 123 MET cc_start: 0.8129 (mmm) cc_final: 0.7832 (mmt) REVERT: C 206 ARG cc_start: 0.7582 (ttm170) cc_final: 0.7246 (ttm-80) REVERT: D 158 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7849 (mtpp) REVERT: D 179 ARG cc_start: 0.7395 (ptt180) cc_final: 0.7074 (ttm110) REVERT: D 238 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7658 (mtt90) REVERT: D 256 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.7023 (ptm160) REVERT: D 507 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: D 518 HIS cc_start: 0.7812 (p-80) cc_final: 0.7580 (p-80) outliers start: 21 outliers final: 14 residues processed: 209 average time/residue: 0.1193 time to fit residues: 35.7521 Evaluate side-chains 203 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 652 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 130 optimal weight: 2.9990 chunk 30 optimal weight: 0.0060 chunk 107 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 173 HIS A 353 GLN B 225 ASN D 332 ASN D 490 ASN D 614 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.150216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.111728 restraints weight = 37532.584| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.01 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14620 Z= 0.229 Angle : 0.652 8.148 19817 Z= 0.324 Chirality : 0.048 0.171 2181 Planarity : 0.005 0.051 2550 Dihedral : 8.472 140.221 2008 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.82 % Allowed : 9.73 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1780 helix: 0.23 (0.19), residues: 784 sheet: 0.06 (0.29), residues: 320 loop : -0.41 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 372 TYR 0.017 0.002 TYR D 310 PHE 0.022 0.002 PHE D 342 TRP 0.015 0.002 TRP B 79 HIS 0.007 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00565 (14620) covalent geometry : angle 0.65217 (19817) hydrogen bonds : bond 0.04364 ( 640) hydrogen bonds : angle 4.73424 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: B 28 ARG cc_start: 0.8146 (ttm170) cc_final: 0.7928 (ttm-80) REVERT: B 176 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: C 123 MET cc_start: 0.8224 (mmm) cc_final: 0.7891 (mmt) REVERT: C 206 ARG cc_start: 0.7265 (ttm170) cc_final: 0.6966 (ttm-80) REVERT: D 256 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7086 (ptm160) REVERT: D 507 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6616 (tp30) outliers start: 28 outliers final: 18 residues processed: 209 average time/residue: 0.1309 time to fit residues: 39.0628 Evaluate side-chains 207 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 534 ARG Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 652 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 78 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 28 optimal weight: 0.0470 chunk 171 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 353 GLN B 225 ASN D 614 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.151724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.114005 restraints weight = 37538.085| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.65 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14620 Z= 0.149 Angle : 0.586 8.655 19817 Z= 0.288 Chirality : 0.045 0.151 2181 Planarity : 0.004 0.049 2550 Dihedral : 8.300 140.589 2008 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.49 % Allowed : 10.32 % Favored : 88.19 % 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: 0.03 (0.20), residues: 1780 helix: 0.40 (0.19), residues: 788 sheet: 0.14 (0.28), residues: 324 loop : -0.30 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 372 TYR 0.013 0.001 TYR D 310 PHE 0.016 0.001 PHE D 342 TRP 0.014 0.001 TRP B 79 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00358 (14620) covalent geometry : angle 0.58567 (19817) hydrogen bonds : bond 0.03555 ( 640) hydrogen bonds : angle 4.59015 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.405 Fit side-chains REVERT: A 72 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: B 176 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7776 (mtp) REVERT: C 206 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6980 (ttm-80) REVERT: D 238 ARG cc_start: 0.7817 (mmt90) cc_final: 0.7562 (mtt90) REVERT: D 507 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: D 575 ASN cc_start: 0.8317 (m-40) cc_final: 0.7852 (m-40) outliers start: 23 outliers final: 15 residues processed: 194 average time/residue: 0.1254 time to fit residues: 34.2801 Evaluate side-chains 199 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 471 PHE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 605 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 17 optimal weight: 0.4980 chunk 112 optimal weight: 0.0010 chunk 153 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 91 optimal weight: 0.0970 chunk 173 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 225 ASN C 162 ASN D 614 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.154338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.116464 restraints weight = 39283.027| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 5.09 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14620 Z= 0.095 Angle : 0.538 8.132 19817 Z= 0.261 Chirality : 0.042 0.134 2181 Planarity : 0.004 0.049 2550 Dihedral : 7.892 137.215 2008 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.17 % Allowed : 11.16 % Favored : 87.67 % 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: 0.39 (0.21), residues: 1780 helix: 0.73 (0.19), residues: 789 sheet: 0.26 (0.28), residues: 325 loop : -0.11 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 28 TYR 0.009 0.001 TYR C 306 PHE 0.012 0.001 PHE D 175 TRP 0.012 0.001 TRP B 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00211 (14620) covalent geometry : angle 0.53838 (19817) hydrogen bonds : bond 0.02778 ( 640) hydrogen bonds : angle 4.41422 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.433 Fit side-chains REVERT: A 72 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: B 176 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7610 (mtp) REVERT: C 206 ARG cc_start: 0.7158 (ttm170) cc_final: 0.6875 (ttm-80) REVERT: D 238 ARG cc_start: 0.7818 (mmt90) cc_final: 0.7589 (mtt90) REVERT: D 507 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6556 (tp30) REVERT: D 575 ASN cc_start: 0.8262 (m-40) cc_final: 0.7897 (m-40) outliers start: 18 outliers final: 12 residues processed: 200 average time/residue: 0.1193 time to fit residues: 34.3840 Evaluate side-chains 198 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 644 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 106 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 167 optimal weight: 0.0980 chunk 109 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN D 153 GLN D 614 HIS D 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.153810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.119088 restraints weight = 40268.481| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.32 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14620 Z= 0.108 Angle : 0.556 8.654 19817 Z= 0.270 Chirality : 0.043 0.148 2181 Planarity : 0.004 0.047 2550 Dihedral : 7.862 136.414 2008 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.23 % Allowed : 11.88 % Favored : 86.89 % 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: 0.47 (0.21), residues: 1780 helix: 0.80 (0.19), residues: 791 sheet: 0.28 (0.28), residues: 325 loop : -0.07 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 28 TYR 0.011 0.001 TYR D 310 PHE 0.012 0.001 PHE D 342 TRP 0.011 0.001 TRP B 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00250 (14620) covalent geometry : angle 0.55584 (19817) hydrogen bonds : bond 0.02975 ( 640) hydrogen bonds : angle 4.42551 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.474 Fit side-chains REVERT: A 72 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: A 132 MET cc_start: 0.8407 (ptm) cc_final: 0.8133 (ptm) REVERT: B 80 ASP cc_start: 0.8044 (m-30) cc_final: 0.7816 (m-30) REVERT: B 176 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7674 (mtp) REVERT: B 283 MET cc_start: 0.8262 (mmt) cc_final: 0.8005 (mmm) REVERT: C 123 MET cc_start: 0.8309 (mmp) cc_final: 0.8040 (mmt) REVERT: C 206 ARG cc_start: 0.7320 (ttm170) cc_final: 0.7071 (ttm-80) REVERT: D 238 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7549 (mtt90) REVERT: D 507 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6525 (tp30) REVERT: D 575 ASN cc_start: 0.8241 (m-40) cc_final: 0.7860 (m-40) outliers start: 19 outliers final: 14 residues processed: 187 average time/residue: 0.1306 time to fit residues: 34.6327 Evaluate side-chains 193 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 162 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 163 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 131 optimal weight: 0.0050 chunk 105 optimal weight: 0.0570 chunk 127 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.4312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 225 ASN D 614 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.153949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.116607 restraints weight = 39376.434| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.92 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14620 Z= 0.106 Angle : 0.552 8.090 19817 Z= 0.267 Chirality : 0.043 0.134 2181 Planarity : 0.004 0.047 2550 Dihedral : 7.812 136.732 2008 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.30 % Allowed : 12.07 % Favored : 86.63 % 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: 0.52 (0.21), residues: 1780 helix: 0.84 (0.19), residues: 791 sheet: 0.30 (0.28), residues: 325 loop : -0.06 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 28 TYR 0.011 0.001 TYR D 310 PHE 0.012 0.001 PHE D 342 TRP 0.011 0.001 TRP B 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00245 (14620) covalent geometry : angle 0.55161 (19817) hydrogen bonds : bond 0.02924 ( 640) hydrogen bonds : angle 4.41004 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.366 Fit side-chains REVERT: A 72 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: A 132 MET cc_start: 0.8450 (ptm) cc_final: 0.8187 (ptm) REVERT: B 80 ASP cc_start: 0.7986 (m-30) cc_final: 0.7756 (m-30) REVERT: B 176 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7585 (mtp) REVERT: B 283 MET cc_start: 0.8241 (mmt) cc_final: 0.7983 (mmm) REVERT: C 206 ARG cc_start: 0.7181 (ttm170) cc_final: 0.6889 (ttm-80) REVERT: C 291 LYS cc_start: 0.7701 (tttp) cc_final: 0.7390 (mmtt) REVERT: D 238 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7560 (mtt90) REVERT: D 507 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6575 (tp30) REVERT: D 575 ASN cc_start: 0.8224 (m-40) cc_final: 0.7859 (m-40) outliers start: 20 outliers final: 17 residues processed: 191 average time/residue: 0.1282 time to fit residues: 34.4998 Evaluate side-chains 199 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 507 GLU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 678 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 131 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 225 ASN D 614 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.152442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.114893 restraints weight = 29555.548| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.98 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14620 Z= 0.144 Angle : 0.583 8.168 19817 Z= 0.286 Chirality : 0.045 0.137 2181 Planarity : 0.004 0.046 2550 Dihedral : 7.924 138.491 2008 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.30 % Allowed : 12.20 % Favored : 86.50 % 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: 0.45 (0.21), residues: 1780 helix: 0.82 (0.19), residues: 777 sheet: 0.25 (0.28), residues: 325 loop : -0.11 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.014 0.001 TYR D 310 PHE 0.016 0.001 PHE D 342 TRP 0.012 0.001 TRP B 79 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00349 (14620) covalent geometry : angle 0.58336 (19817) hydrogen bonds : bond 0.03389 ( 640) hydrogen bonds : angle 4.50408 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.03 seconds wall clock time: 55 minutes 16.44 seconds (3316.44 seconds total)