Starting phenix.real_space_refine on Sat Feb 7 03:55:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vkr_65140/02_2026/9vkr_65140.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vkr_65140/02_2026/9vkr_65140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vkr_65140/02_2026/9vkr_65140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vkr_65140/02_2026/9vkr_65140.map" model { file = "/net/cci-nas-00/data/ceres_data/9vkr_65140/02_2026/9vkr_65140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vkr_65140/02_2026/9vkr_65140.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 16 5.49 5 Mg 5 5.21 5 S 72 5.16 5 C 18463 2.51 5 N 5162 2.21 5 O 5842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s 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: 29560 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3920 Classifications: {'peptide': 518} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 495} Chain: "B" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3959 Classifications: {'peptide': 523} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain: "C" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4050 Classifications: {'peptide': 535} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 510} Chain breaks: 1 Chain: "D" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3600 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "E" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3592 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 443} Chain: "F" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3583 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 442} Chain: "G" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2315 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 11, 'TRANS': 294} Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "b" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 588 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "d" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2850 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 10, 'TRANS': 371} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.66, per 1000 atoms: 0.23 Number of scatterers: 29560 At special positions: 0 Unit cell: (124.64, 145.16, 186.2, 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 72 16.00 P 16 15.00 Mg 5 11.99 O 5842 8.00 N 5162 7.00 C 18463 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7090 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 26 sheets defined 51.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.742A pdb=" N ILE A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.973A pdb=" N PHE A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.555A pdb=" N VAL A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.608A pdb=" N ALA A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.653A pdb=" N GLU A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 264 Proline residue: A 250 - end of helix removed outlier: 3.831A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 4.114A pdb=" N GLN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.635A pdb=" N LEU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.887A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 478 Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.956A pdb=" N LEU A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'B' and resid 7 through 21 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.999A pdb=" N PHE B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 107 " --> pdb=" O ASP B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.883A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.529A pdb=" N VAL B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.793A pdb=" N THR B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 227 through 230 removed outlier: 4.034A pdb=" N GLU B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 242 through 264 removed outlier: 3.550A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.786A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.830A pdb=" N GLN B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.700A pdb=" N HIS B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.565A pdb=" N GLY B 320 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.505A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 392 through 404 Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.779A pdb=" N LEU B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'C' and resid 7 through 22 removed outlier: 3.923A pdb=" N ILE C 11 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.921A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 107 " --> pdb=" O ASP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.763A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.545A pdb=" N ALA C 226 " --> pdb=" O THR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 230 removed outlier: 4.052A pdb=" N GLU C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 250 - end of helix removed outlier: 3.712A pdb=" N GLY C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 4.057A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.593A pdb=" N HIS C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.823A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.599A pdb=" N GLY C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.258A pdb=" N LEU C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.760A pdb=" N VAL D 95 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.760A pdb=" N LEU D 131 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 149 Processing helix chain 'D' and resid 166 through 179 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 246 removed outlier: 3.536A pdb=" N ARG D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU D 233 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 272 removed outlier: 4.086A pdb=" N THR D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 312 through 315 Processing helix chain 'D' and resid 318 through 324 removed outlier: 3.876A pdb=" N THR D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 removed outlier: 3.949A pdb=" N LEU D 328 " --> pdb=" O PHE D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 335 through 341 removed outlier: 3.643A pdb=" N LYS D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 363 through 390 removed outlier: 4.965A pdb=" N ASP D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'D' and resid 396 through 413 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 420 through 425 Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 452 through 457 removed outlier: 3.650A pdb=" N PHE D 456 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE D 457 " --> pdb=" O GLN D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 473 removed outlier: 3.524A pdb=" N GLY D 473 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.693A pdb=" N VAL E 95 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS E 96 " --> pdb=" O ASP E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 142 through 148 Processing helix chain 'E' and resid 166 through 182 removed outlier: 3.605A pdb=" N LEU E 170 " --> pdb=" O GLY E 166 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 182 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 208 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 229 removed outlier: 3.697A pdb=" N ARG E 228 " --> pdb=" O PRO E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 245 Processing helix chain 'E' and resid 256 through 271 removed outlier: 4.032A pdb=" N PHE E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 283 through 293 Processing helix chain 'E' and resid 311 through 315 Processing helix chain 'E' and resid 318 through 325 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 363 through 383 removed outlier: 3.564A pdb=" N TYR E 367 " --> pdb=" O GLY E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 Processing helix chain 'E' and resid 396 through 413 Processing helix chain 'E' and resid 417 through 423 removed outlier: 4.108A pdb=" N GLN E 422 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 452 through 457 Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.773A pdb=" N VAL F 95 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS F 96 " --> pdb=" O ASP F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 96' Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 142 through 149 Processing helix chain 'F' and resid 166 through 179 removed outlier: 3.527A pdb=" N LEU F 170 " --> pdb=" O GLY F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 208 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 230 through 245 Processing helix chain 'F' and resid 257 through 272 removed outlier: 3.818A pdb=" N THR F 261 " --> pdb=" O ILE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 280 Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 312 through 315 Processing helix chain 'F' and resid 318 through 325 removed outlier: 3.758A pdb=" N THR F 324 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE F 325 " --> pdb=" O PRO F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 363 through 383 Processing helix chain 'F' and resid 384 through 391 Processing helix chain 'F' and resid 396 through 413 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 420 through 425 Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 461 through 473 Processing helix chain 'G' and resid 3 through 60 removed outlier: 3.860A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Proline residue: G 45 - end of helix removed outlier: 3.908A pdb=" N THR G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.990A pdb=" N GLU G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.800A pdb=" N LEU G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 164 removed outlier: 3.578A pdb=" N GLY G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 306 Proline residue: G 236 - end of helix removed outlier: 3.739A pdb=" N LEU G 239 " --> pdb=" O LEU G 235 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA G 305 " --> pdb=" O ALA G 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 100 Processing helix chain 'H' and resid 103 through 117 Processing helix chain 'b' and resid 90 through 103 Processing helix chain 'b' and resid 105 through 148 removed outlier: 3.903A pdb=" N GLY b 146 " --> pdb=" O GLU b 142 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU b 147 " --> pdb=" O VAL b 143 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU b 148 " --> pdb=" O THR b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 165 Processing helix chain 'd' and resid 67 through 138 removed outlier: 3.611A pdb=" N GLN d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER d 84 " --> pdb=" O ALA d 80 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS d 85 " --> pdb=" O VAL d 81 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN d 86 " --> pdb=" O GLN d 82 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY d 119 " --> pdb=" O ARG d 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP d 120 " --> pdb=" O GLN d 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA d 138 " --> pdb=" O ARG d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 157 Processing helix chain 'd' and resid 177 through 194 removed outlier: 4.529A pdb=" N GLU d 181 " --> pdb=" O ALA d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 197 No H-bonds generated for 'chain 'd' and resid 195 through 197' Processing helix chain 'd' and resid 198 through 219 Processing helix chain 'd' and resid 219 through 228 removed outlier: 3.836A pdb=" N ARG d 223 " --> pdb=" O GLU d 219 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 247 Processing helix chain 'd' and resid 251 through 264 removed outlier: 3.528A pdb=" N ALA d 264 " --> pdb=" O SER d 260 " (cutoff:3.500A) Processing helix chain 'd' and resid 268 through 292 removed outlier: 4.337A pdb=" N LEU d 272 " --> pdb=" O ALA d 268 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE d 273 " --> pdb=" O SER d 269 " (cutoff:3.500A) Processing helix chain 'd' and resid 293 through 311 Processing helix chain 'd' and resid 311 through 319 Processing helix chain 'd' and resid 324 through 337 removed outlier: 3.729A pdb=" N ARG d 328 " --> pdb=" O PRO d 324 " (cutoff:3.500A) Processing helix chain 'd' and resid 341 through 354 Processing helix chain 'd' and resid 359 through 376 Processing helix chain 'd' and resid 389 through 405 Processing helix chain 'd' and resid 416 through 419 Processing helix chain 'd' and resid 434 through 445 removed outlier: 3.703A pdb=" N ARG d 438 " --> pdb=" O SER d 434 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 69 removed outlier: 4.052A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS A 43 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A 69 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 63 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP E 79 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU E 40 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG E 64 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N HIS E 57 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU E 62 " --> pdb=" O HIS E 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG E 15 " --> pdb=" O ASP E 22 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL E 13 " --> pdb=" O GLU E 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.346A pdb=" N ILE A 111 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG A 203 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL A 270 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A 205 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 69 removed outlier: 4.108A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 94 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N HIS B 43 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP F 79 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU F 40 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG F 64 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS F 57 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU F 62 " --> pdb=" O HIS F 57 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG F 15 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL F 13 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.268A pdb=" N ARG B 203 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL B 270 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE B 205 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP B 272 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL B 207 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.453A pdb=" N ILE B 162 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 31 through 38 removed outlier: 6.547A pdb=" N HIS C 43 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU C 69 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLU C 96 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU C 57 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR C 94 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.411A pdb=" N ILE C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG C 203 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL C 270 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE C 205 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP C 272 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL C 207 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 271 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 534 through 541 removed outlier: 5.844A pdb=" N GLY C 535 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA G 204 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLU C 537 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET G 206 " --> pdb=" O GLU C 537 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL C 539 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL G 208 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 541 " --> pdb=" O VAL G 208 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR G 210 " --> pdb=" O VAL C 541 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU G 183 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THR G 188 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL G 116 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N TRP G 138 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 17 removed outlier: 6.603A pdb=" N ASP D 22 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL D 16 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU D 62 " --> pdb=" O HIS D 57 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N HIS D 57 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG D 64 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU D 40 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP D 79 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 88 through 91 removed outlier: 4.186A pdb=" N GLU D 117 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 100 removed outlier: 6.684A pdb=" N ILE D 157 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL D 309 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU D 159 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 137 through 138 removed outlier: 4.085A pdb=" N TYR D 151 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 88 through 91 removed outlier: 4.293A pdb=" N GLU E 117 " --> pdb=" O VAL E 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AC1, first strand: chain 'E' and resid 99 through 101 removed outlier: 6.264A pdb=" N ILE E 157 " --> pdb=" O GLN E 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 137 through 138 removed outlier: 4.325A pdb=" N TYR E 151 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 88 through 91 removed outlier: 4.252A pdb=" N GLU F 117 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 99 through 100 removed outlier: 6.824A pdb=" N SER F 186 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL F 217 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE F 188 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLY F 219 " --> pdb=" O PHE F 188 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLY F 190 " --> pdb=" O GLY F 219 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE F 157 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL F 309 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU F 159 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 137 through 138 removed outlier: 4.441A pdb=" N TYR F 151 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 14 through 19 removed outlier: 3.930A pdb=" N TRP H 16 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 77 " --> pdb=" O ASP H 5 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 78 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE H 69 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.640A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA H 49 " --> pdb=" O ILE H 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.640A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) 1612 hydrogen bonds defined for protein. 4602 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: 5.94 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10184 1.34 - 1.46: 4184 1.46 - 1.57: 15492 1.57 - 1.69: 26 1.69 - 1.81: 128 Bond restraints: 30014 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP F 600 " pdb=" C5 ADP F 600 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C5 ADP D 600 " pdb=" C6 ADP D 600 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 ADP F 600 " pdb=" C6 ADP F 600 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" N VAL F 210 " pdb=" CA VAL F 210 " ideal model delta sigma weight residual 1.459 1.492 -0.034 9.10e-03 1.21e+04 1.36e+01 ... (remaining 30009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 40254 2.32 - 4.65: 455 4.65 - 6.97: 31 6.97 - 9.29: 9 9.29 - 11.62: 7 Bond angle restraints: 40756 Sorted by residual: angle pdb=" PB ATP E 600 " pdb=" O3B ATP E 600 " pdb=" PG ATP E 600 " ideal model delta sigma weight residual 139.87 132.35 7.52 1.00e+00 1.00e+00 5.65e+01 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 133.41 6.46 1.00e+00 1.00e+00 4.17e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 133.64 6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 134.06 5.81 1.00e+00 1.00e+00 3.37e+01 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 132.00 4.83 1.00e+00 1.00e+00 2.33e+01 ... (remaining 40751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 17782 23.81 - 47.61: 434 47.61 - 71.42: 51 71.42 - 95.23: 14 95.23 - 119.04: 2 Dihedral angle restraints: 18283 sinusoidal: 7252 harmonic: 11031 Sorted by residual: dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -179.03 119.04 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 -162.02 102.01 1 2.00e+01 2.50e-03 2.90e+01 dihedral pdb=" CA PHE F 218 " pdb=" C PHE F 218 " pdb=" N GLY F 219 " pdb=" CA GLY F 219 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 18280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3613 0.045 - 0.089: 779 0.089 - 0.134: 313 0.134 - 0.178: 22 0.178 - 0.223: 14 Chirality restraints: 4741 Sorted by residual: chirality pdb=" CA ILE E 387 " pdb=" N ILE E 387 " pdb=" C ILE E 387 " pdb=" CB ILE E 387 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE E 459 " pdb=" N ILE E 459 " pdb=" C ILE E 459 " pdb=" CB ILE E 459 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C3' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C4' ADP D 600 " pdb=" O3' ADP D 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4738 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG d 110 " -0.238 9.50e-02 1.11e+02 1.07e-01 7.05e+00 pdb=" NE ARG d 110 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG d 110 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG d 110 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG d 110 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 76 " -0.172 9.50e-02 1.11e+02 7.71e-02 3.66e+00 pdb=" NE ARG F 76 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG F 76 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG F 76 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 76 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 121 " -0.167 9.50e-02 1.11e+02 7.51e-02 3.48e+00 pdb=" NE ARG G 121 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG G 121 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG G 121 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 121 " -0.005 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 140 2.59 - 3.17: 24105 3.17 - 3.74: 42921 3.74 - 4.32: 60781 4.32 - 4.90: 104623 Nonbonded interactions: 232570 Sorted by model distance: nonbonded pdb="MG MG C 603 " pdb=" O3B ADP D 600 " model vdw 2.012 2.170 nonbonded pdb=" OG1 THR C 179 " pdb="MG MG C 602 " model vdw 2.020 2.170 nonbonded pdb=" OG1 THR A 179 " pdb="MG MG A 601 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR B 179 " pdb="MG MG B 601 " model vdw 2.146 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 2.195 2.170 ... (remaining 232565 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 515 or resid 517 or resid 519 through 522 or res \ id 601)) selection = (chain 'B' and (resid 6 through 515 or resid 517 or resid 519 through 522 or res \ id 601)) selection = (chain 'C' and (resid 6 through 515 or resid 532 or resid 534 or resid 537 or re \ sid 541 or resid 543 or resid 603)) } ncs_group { reference = (chain 'D' and resid 9 through 476) selection = (chain 'E' and resid 9 through 476) selection = (chain 'F' and resid 9 through 476) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.230 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.010 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.004 0.111 30014 Z= 0.255 Angle : 0.573 11.617 40756 Z= 0.352 Chirality : 0.044 0.223 4741 Planarity : 0.004 0.107 5356 Dihedral : 10.612 119.036 11193 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.34 (0.14), residues: 3850 helix: 2.15 (0.13), residues: 1698 sheet: 0.80 (0.22), residues: 570 loop : -0.47 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 110 TYR 0.011 0.001 TYR G 92 PHE 0.009 0.001 PHE F 440 TRP 0.008 0.001 TRP A 247 HIS 0.004 0.001 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00390 (30014) covalent geometry : angle 0.57258 (40756) hydrogen bonds : bond 0.18019 ( 1589) hydrogen bonds : angle 6.45085 ( 4602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 329 time to evaluate : 1.085 Fit side-chains REVERT: A 45 GLU cc_start: 0.8641 (tt0) cc_final: 0.8434 (tt0) REVERT: A 462 GLU cc_start: 0.8064 (mp0) cc_final: 0.7845 (pm20) REVERT: A 485 ASP cc_start: 0.7511 (t0) cc_final: 0.7068 (m-30) REVERT: B 45 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7948 (mm-30) REVERT: B 65 VAL cc_start: 0.8825 (t) cc_final: 0.8517 (p) REVERT: B 358 ASP cc_start: 0.8047 (m-30) cc_final: 0.7741 (p0) REVERT: B 384 LYS cc_start: 0.8263 (mttp) cc_final: 0.8038 (mttt) REVERT: B 462 GLU cc_start: 0.8305 (mp0) cc_final: 0.8104 (pt0) REVERT: C 45 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8048 (mm-30) REVERT: C 388 GLU cc_start: 0.7432 (tt0) cc_final: 0.7075 (mt-10) REVERT: D 27 ARG cc_start: 0.7667 (ttp80) cc_final: 0.6903 (tpm170) REVERT: D 136 GLU cc_start: 0.8371 (tt0) cc_final: 0.7665 (mp0) REVERT: D 288 MET cc_start: 0.8543 (tpp) cc_final: 0.8271 (tpt) REVERT: D 399 ASP cc_start: 0.7892 (m-30) cc_final: 0.7637 (m-30) REVERT: D 467 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7438 (tmtm) REVERT: E 93 ASP cc_start: 0.8451 (p0) cc_final: 0.8244 (p0) REVERT: E 426 GLN cc_start: 0.7874 (mm-40) cc_final: 0.6928 (tt0) REVERT: F 445 LYS cc_start: 0.7855 (mmtp) cc_final: 0.7365 (mtmm) REVERT: F 454 GLN cc_start: 0.8195 (mm110) cc_final: 0.7329 (mp-120) REVERT: G 194 LEU cc_start: 0.8038 (mt) cc_final: 0.7477 (tp) REVERT: G 287 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8696 (tm130) REVERT: H 66 ASP cc_start: 0.6405 (p0) cc_final: 0.5951 (p0) REVERT: d 90 GLN cc_start: 0.6715 (tt0) cc_final: 0.6280 (mt0) outliers start: 4 outliers final: 0 residues processed: 333 average time/residue: 0.8015 time to fit residues: 303.8204 Evaluate side-chains 197 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0020 chunk 298 optimal weight: 0.8980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN C 68 ASN C 191 GLN C 436 ASN E 366 HIS E 454 GLN F 85 ASN F 256 ASN b 120 GLN d 105 GLN d 109 GLN d 111 GLN d 136 HIS d 176 HIS d 243 ASN d 425 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.084954 restraints weight = 43528.268| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.07 r_work: 0.2898 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30014 Z= 0.117 Angle : 0.503 12.606 40756 Z= 0.262 Chirality : 0.041 0.168 4741 Planarity : 0.004 0.045 5356 Dihedral : 6.469 107.287 4342 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.16 % Allowed : 6.32 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.56 (0.14), residues: 3850 helix: 2.39 (0.13), residues: 1728 sheet: 0.94 (0.23), residues: 519 loop : -0.45 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 153 TYR 0.012 0.001 TYR G 92 PHE 0.018 0.001 PHE G 231 TRP 0.012 0.001 TRP H 63 HIS 0.004 0.001 HIS d 176 Details of bonding type rmsd covalent geometry : bond 0.00243 (30014) covalent geometry : angle 0.50337 (40756) hydrogen bonds : bond 0.05078 ( 1589) hydrogen bonds : angle 4.72059 ( 4602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 1.126 Fit side-chains REVERT: A 98 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8874 (tt) REVERT: A 485 ASP cc_start: 0.7998 (t0) cc_final: 0.7424 (m-30) REVERT: B 1 MET cc_start: 0.6109 (tpt) cc_final: 0.5557 (ptt) REVERT: B 45 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8143 (mm-30) REVERT: B 65 VAL cc_start: 0.8670 (t) cc_final: 0.8340 (p) REVERT: B 358 ASP cc_start: 0.8165 (m-30) cc_final: 0.7917 (p0) REVERT: B 384 LYS cc_start: 0.8550 (mttp) cc_final: 0.8307 (mttt) REVERT: C 45 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8276 (mm-30) REVERT: C 388 GLU cc_start: 0.7746 (tt0) cc_final: 0.7370 (mt-10) REVERT: D 27 ARG cc_start: 0.7725 (ttp80) cc_final: 0.6972 (tpm170) REVERT: D 136 GLU cc_start: 0.8401 (tt0) cc_final: 0.7588 (mp0) REVERT: D 288 MET cc_start: 0.8637 (tpp) cc_final: 0.8389 (tpt) REVERT: D 467 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7514 (tmtm) REVERT: E 426 GLN cc_start: 0.7937 (mm-40) cc_final: 0.6992 (tt0) REVERT: E 434 LYS cc_start: 0.7475 (mtmm) cc_final: 0.7190 (mttm) REVERT: F 398 GLU cc_start: 0.7793 (mp0) cc_final: 0.7501 (pt0) REVERT: F 445 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7539 (mtmm) REVERT: F 454 GLN cc_start: 0.8215 (mm110) cc_final: 0.7528 (mp-120) REVERT: G 108 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6310 (tpp80) REVERT: G 194 LEU cc_start: 0.8094 (mt) cc_final: 0.7463 (tp) REVERT: G 287 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8575 (tm130) REVERT: H 1 MET cc_start: 0.2192 (OUTLIER) cc_final: 0.0017 (mpp) REVERT: H 66 ASP cc_start: 0.6402 (p0) cc_final: 0.5734 (p0) REVERT: d 90 GLN cc_start: 0.6496 (tt0) cc_final: 0.6086 (mt0) outliers start: 36 outliers final: 17 residues processed: 230 average time/residue: 0.7611 time to fit residues: 201.4042 Evaluate side-chains 202 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain d residue 166 ARG Chi-restraints excluded: chain d residue 269 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 270 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 251 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 455 HIS C 335 ASN C 436 ASN C 502 ASN d 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.080798 restraints weight = 43827.364| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.06 r_work: 0.2825 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30014 Z= 0.173 Angle : 0.552 13.491 40756 Z= 0.286 Chirality : 0.043 0.164 4741 Planarity : 0.004 0.051 5356 Dihedral : 6.578 92.874 4342 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Rotamer: Outliers : 1.64 % Allowed : 7.12 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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 (0.14), residues: 3850 helix: 2.27 (0.12), residues: 1731 sheet: 0.84 (0.22), residues: 530 loop : -0.61 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 228 TYR 0.014 0.001 TYR A 439 PHE 0.016 0.002 PHE F 260 TRP 0.013 0.001 TRP H 63 HIS 0.004 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00419 (30014) covalent geometry : angle 0.55232 (40756) hydrogen bonds : bond 0.06302 ( 1589) hydrogen bonds : angle 4.68370 ( 4602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 1.194 Fit side-chains REVERT: A 98 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8954 (tt) REVERT: A 485 ASP cc_start: 0.8104 (t0) cc_final: 0.7540 (m-30) REVERT: B 45 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8209 (mm-30) REVERT: B 65 VAL cc_start: 0.8847 (t) cc_final: 0.8639 (p) REVERT: B 358 ASP cc_start: 0.8205 (m-30) cc_final: 0.7991 (p0) REVERT: B 384 LYS cc_start: 0.8690 (mttp) cc_final: 0.8446 (mttt) REVERT: C 45 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8259 (mm-30) REVERT: C 388 GLU cc_start: 0.7903 (tt0) cc_final: 0.7527 (mt-10) REVERT: C 436 ASN cc_start: 0.8797 (t0) cc_final: 0.8590 (t0) REVERT: D 27 ARG cc_start: 0.7811 (ttp80) cc_final: 0.6979 (tpm170) REVERT: D 136 GLU cc_start: 0.8402 (tt0) cc_final: 0.7485 (mp0) REVERT: D 180 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8281 (ttm170) REVERT: D 288 MET cc_start: 0.8682 (tpp) cc_final: 0.8415 (tpt) REVERT: D 467 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7469 (tmtm) REVERT: E 46 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.6885 (mmt) REVERT: E 197 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: E 411 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.5989 (mtp85) REVERT: E 426 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7021 (tt0) REVERT: F 365 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8147 (tp30) REVERT: F 445 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7593 (mtmt) REVERT: F 454 GLN cc_start: 0.8257 (mm110) cc_final: 0.7515 (mp-120) REVERT: G 108 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6210 (tpp80) REVERT: G 194 LEU cc_start: 0.8284 (mt) cc_final: 0.7590 (tp) REVERT: d 90 GLN cc_start: 0.6540 (tt0) cc_final: 0.6068 (mt0) REVERT: d 104 GLU cc_start: 0.8347 (tp30) cc_final: 0.8079 (mt-10) outliers start: 51 outliers final: 20 residues processed: 220 average time/residue: 0.7804 time to fit residues: 198.0794 Evaluate side-chains 201 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 411 ARG Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain d residue 166 ARG Chi-restraints excluded: chain d residue 269 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 10 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 311 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 342 optimal weight: 0.0050 chunk 239 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 0.0870 chunk 217 optimal weight: 3.9990 overall best weight: 1.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 ASN C 191 GLN C 335 ASN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.082515 restraints weight = 43342.829| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.06 r_work: 0.2854 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30014 Z= 0.126 Angle : 0.491 12.951 40756 Z= 0.255 Chirality : 0.041 0.156 4741 Planarity : 0.004 0.047 5356 Dihedral : 6.377 87.872 4342 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.08 % Rotamer: Outliers : 1.58 % Allowed : 7.61 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.48 (0.14), residues: 3850 helix: 2.44 (0.12), residues: 1718 sheet: 0.79 (0.22), residues: 527 loop : -0.60 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.012 0.001 TYR G 92 PHE 0.011 0.001 PHE d 150 TRP 0.011 0.001 TRP H 63 HIS 0.002 0.001 HIS D 327 Details of bonding type rmsd covalent geometry : bond 0.00285 (30014) covalent geometry : angle 0.49053 (40756) hydrogen bonds : bond 0.05257 ( 1589) hydrogen bonds : angle 4.42713 ( 4602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 1.241 Fit side-chains REVERT: A 98 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8943 (tt) REVERT: A 485 ASP cc_start: 0.8084 (t0) cc_final: 0.7566 (m-30) REVERT: A 517 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.7770 (p) REVERT: B 1 MET cc_start: 0.6054 (tpt) cc_final: 0.5230 (ptt) REVERT: B 45 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8216 (mm-30) REVERT: B 384 LYS cc_start: 0.8707 (mttp) cc_final: 0.8457 (mttt) REVERT: C 45 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8222 (mm-30) REVERT: C 72 ARG cc_start: 0.8358 (mtp85) cc_final: 0.7929 (mmm160) REVERT: C 388 GLU cc_start: 0.7837 (tt0) cc_final: 0.7467 (mt-10) REVERT: D 27 ARG cc_start: 0.7778 (ttp80) cc_final: 0.6985 (tpm170) REVERT: D 136 GLU cc_start: 0.8363 (tt0) cc_final: 0.7476 (mp0) REVERT: D 180 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8211 (ttm170) REVERT: D 288 MET cc_start: 0.8664 (tpp) cc_final: 0.8394 (tpt) REVERT: D 306 MET cc_start: 0.9247 (ttt) cc_final: 0.9017 (ttt) REVERT: D 457 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: D 467 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7425 (tmtm) REVERT: E 46 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.6799 (mmt) REVERT: E 197 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: E 411 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.5982 (mtp85) REVERT: E 426 GLN cc_start: 0.7980 (mm-40) cc_final: 0.6984 (tt0) REVERT: F 365 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8049 (tp30) REVERT: F 398 GLU cc_start: 0.7524 (mp0) cc_final: 0.7319 (pt0) REVERT: F 445 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7491 (mtmt) REVERT: F 454 GLN cc_start: 0.8216 (mm110) cc_final: 0.7499 (mp-120) REVERT: G 108 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6382 (tpp80) REVERT: G 194 LEU cc_start: 0.8274 (mt) cc_final: 0.7580 (tp) REVERT: G 290 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: d 90 GLN cc_start: 0.6557 (tt0) cc_final: 0.6073 (mt0) REVERT: d 104 GLU cc_start: 0.8407 (tp30) cc_final: 0.8101 (tp30) outliers start: 49 outliers final: 21 residues processed: 220 average time/residue: 0.8262 time to fit residues: 209.7723 Evaluate side-chains 201 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 411 ARG Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain d residue 166 ARG Chi-restraints excluded: chain d residue 269 SER Chi-restraints excluded: chain d residue 335 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 37 optimal weight: 6.9990 chunk 125 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 chunk 168 optimal weight: 0.0270 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 195 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 335 ASN G 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085095 restraints weight = 43528.427| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.08 r_work: 0.2903 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30014 Z= 0.093 Angle : 0.444 13.311 40756 Z= 0.230 Chirality : 0.040 0.144 4741 Planarity : 0.003 0.045 5356 Dihedral : 5.997 87.428 4342 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 1.10 % Allowed : 8.48 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.14), residues: 3850 helix: 2.65 (0.13), residues: 1711 sheet: 0.85 (0.22), residues: 526 loop : -0.44 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 237 TYR 0.011 0.001 TYR G 92 PHE 0.012 0.001 PHE d 150 TRP 0.008 0.001 TRP H 62 HIS 0.002 0.000 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00180 (30014) covalent geometry : angle 0.44407 (40756) hydrogen bonds : bond 0.04297 ( 1589) hydrogen bonds : angle 4.13850 ( 4602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 1.069 Fit side-chains REVERT: A 98 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 485 ASP cc_start: 0.8021 (t0) cc_final: 0.7580 (m-30) REVERT: A 517 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7714 (p) REVERT: B 1 MET cc_start: 0.6064 (tpt) cc_final: 0.5689 (OUTLIER) REVERT: B 45 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8233 (mm-30) REVERT: B 384 LYS cc_start: 0.8703 (mttp) cc_final: 0.8454 (mttt) REVERT: C 45 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8224 (mm-30) REVERT: C 72 ARG cc_start: 0.8343 (mtp85) cc_final: 0.7921 (mmm160) REVERT: C 388 GLU cc_start: 0.7795 (tt0) cc_final: 0.7442 (mt-10) REVERT: C 500 LEU cc_start: 0.8812 (tp) cc_final: 0.8569 (tt) REVERT: D 27 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7303 (tpm170) REVERT: D 136 GLU cc_start: 0.8276 (tt0) cc_final: 0.7451 (mp0) REVERT: D 288 MET cc_start: 0.8641 (tpp) cc_final: 0.8429 (tpt) REVERT: D 457 PHE cc_start: 0.7959 (t80) cc_final: 0.7420 (t80) REVERT: D 467 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7384 (tmtm) REVERT: E 426 GLN cc_start: 0.7991 (mm-40) cc_final: 0.6958 (tt0) REVERT: F 398 GLU cc_start: 0.7380 (mp0) cc_final: 0.7158 (pt0) REVERT: F 445 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7304 (mtmt) REVERT: F 454 GLN cc_start: 0.8188 (mm110) cc_final: 0.7498 (mp-120) REVERT: G 108 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6294 (tpp80) REVERT: H 15 ILE cc_start: 0.7018 (mm) cc_final: 0.6649 (pp) REVERT: d 90 GLN cc_start: 0.6533 (tt0) cc_final: 0.6056 (mt0) REVERT: d 104 GLU cc_start: 0.8429 (tp30) cc_final: 0.8059 (mt-10) REVERT: d 166 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7386 (mtm180) outliers start: 34 outliers final: 14 residues processed: 209 average time/residue: 0.8465 time to fit residues: 202.9381 Evaluate side-chains 198 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain d residue 166 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 330 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 335 ASN C 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.080912 restraints weight = 43624.008| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.13 r_work: 0.2827 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30014 Z= 0.161 Angle : 0.522 15.110 40756 Z= 0.271 Chirality : 0.043 0.152 4741 Planarity : 0.004 0.050 5356 Dihedral : 6.309 88.361 4342 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Rotamer: Outliers : 1.45 % Allowed : 8.87 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.53 (0.14), residues: 3850 helix: 2.50 (0.13), residues: 1715 sheet: 0.77 (0.22), residues: 529 loop : -0.57 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 72 TYR 0.014 0.001 TYR A 439 PHE 0.015 0.001 PHE F 260 TRP 0.010 0.001 TRP H 63 HIS 0.004 0.001 HIS D 327 Details of bonding type rmsd covalent geometry : bond 0.00390 (30014) covalent geometry : angle 0.52222 (40756) hydrogen bonds : bond 0.05670 ( 1589) hydrogen bonds : angle 4.36279 ( 4602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 ASP cc_start: 0.8141 (t0) cc_final: 0.7613 (m-30) REVERT: A 517 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.7737 (p) REVERT: B 45 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8229 (mm-30) REVERT: B 384 LYS cc_start: 0.8701 (mttp) cc_final: 0.8442 (mttt) REVERT: C 45 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8218 (mm-30) REVERT: C 72 ARG cc_start: 0.8365 (mtp85) cc_final: 0.7924 (mmm160) REVERT: C 388 GLU cc_start: 0.7832 (tt0) cc_final: 0.7495 (mt-10) REVERT: C 436 ASN cc_start: 0.8768 (t0) cc_final: 0.8564 (t0) REVERT: D 27 ARG cc_start: 0.7807 (ttp80) cc_final: 0.6950 (tpm170) REVERT: D 136 GLU cc_start: 0.8288 (tt0) cc_final: 0.7388 (mp0) REVERT: D 288 MET cc_start: 0.8684 (tpp) cc_final: 0.8427 (tpt) REVERT: D 457 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7448 (t80) REVERT: D 467 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7321 (tmtm) REVERT: E 197 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: E 426 GLN cc_start: 0.8010 (mm-40) cc_final: 0.6980 (tt0) REVERT: F 381 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: F 445 LYS cc_start: 0.7962 (mmtp) cc_final: 0.7482 (mtmt) REVERT: F 454 GLN cc_start: 0.8210 (mm110) cc_final: 0.7472 (mp-120) REVERT: G 108 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6394 (tpp80) REVERT: G 194 LEU cc_start: 0.8452 (mt) cc_final: 0.7687 (tp) REVERT: H 15 ILE cc_start: 0.7010 (mm) cc_final: 0.6529 (pp) REVERT: d 90 GLN cc_start: 0.6556 (tt0) cc_final: 0.6042 (mt0) REVERT: d 104 GLU cc_start: 0.8471 (tp30) cc_final: 0.8151 (tp30) REVERT: d 166 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7440 (mtm180) REVERT: d 265 ARG cc_start: 0.7334 (mtp85) cc_final: 0.7053 (mmm160) outliers start: 45 outliers final: 22 residues processed: 206 average time/residue: 0.8259 time to fit residues: 195.6943 Evaluate side-chains 200 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain d residue 166 ARG Chi-restraints excluded: chain d residue 269 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 313 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 305 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 chunk 310 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN C 191 GLN C 335 ASN G 287 GLN d 105 GLN d 109 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.082748 restraints weight = 43751.808| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.14 r_work: 0.2856 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30014 Z= 0.114 Angle : 0.470 14.200 40756 Z= 0.245 Chirality : 0.041 0.142 4741 Planarity : 0.004 0.047 5356 Dihedral : 6.198 89.524 4342 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Rotamer: Outliers : 1.06 % Allowed : 9.48 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.60 (0.14), residues: 3850 helix: 2.58 (0.13), residues: 1714 sheet: 0.75 (0.22), residues: 528 loop : -0.53 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 88 TYR 0.012 0.001 TYR G 92 PHE 0.010 0.001 PHE F 260 TRP 0.007 0.001 TRP H 63 HIS 0.002 0.001 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00250 (30014) covalent geometry : angle 0.47032 (40756) hydrogen bonds : bond 0.04863 ( 1589) hydrogen bonds : angle 4.23123 ( 4602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 ASP cc_start: 0.8089 (t0) cc_final: 0.7591 (m-30) REVERT: A 517 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7717 (p) REVERT: B 1 MET cc_start: 0.5977 (tpt) cc_final: 0.4883 (ptt) REVERT: B 45 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8226 (mm-30) REVERT: B 384 LYS cc_start: 0.8698 (mttp) cc_final: 0.8434 (mttt) REVERT: C 45 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8201 (mm-30) REVERT: C 72 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7917 (mmm160) REVERT: C 388 GLU cc_start: 0.7853 (tt0) cc_final: 0.7506 (mt-10) REVERT: D 27 ARG cc_start: 0.7778 (ttp80) cc_final: 0.6942 (tpm170) REVERT: D 136 GLU cc_start: 0.8219 (tt0) cc_final: 0.7356 (mp0) REVERT: D 288 MET cc_start: 0.8666 (tpp) cc_final: 0.8430 (tpt) REVERT: D 306 MET cc_start: 0.9238 (ttt) cc_final: 0.8964 (ttt) REVERT: D 457 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: D 467 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7315 (tmtm) REVERT: E 426 GLN cc_start: 0.8003 (mm-40) cc_final: 0.6972 (tt0) REVERT: F 204 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: F 381 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: F 445 LYS cc_start: 0.7823 (mmtp) cc_final: 0.7329 (mtmt) REVERT: F 454 GLN cc_start: 0.8182 (mm110) cc_final: 0.7458 (mp-120) REVERT: G 108 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6340 (tpp80) REVERT: G 194 LEU cc_start: 0.8427 (mt) cc_final: 0.7668 (tp) REVERT: H 15 ILE cc_start: 0.7045 (mm) cc_final: 0.6569 (pp) REVERT: d 90 GLN cc_start: 0.6566 (tt0) cc_final: 0.6046 (mt0) REVERT: d 104 GLU cc_start: 0.8436 (tp30) cc_final: 0.8109 (tp30) REVERT: d 166 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7439 (mtm180) REVERT: d 265 ARG cc_start: 0.7284 (mtp85) cc_final: 0.7019 (mmm160) outliers start: 33 outliers final: 20 residues processed: 199 average time/residue: 0.8092 time to fit residues: 185.0815 Evaluate side-chains 198 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain d residue 166 ARG Chi-restraints excluded: chain d residue 269 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 92 optimal weight: 9.9990 chunk 319 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 356 optimal weight: 0.9990 chunk 222 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 335 ASN d 105 GLN d 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.082304 restraints weight = 43735.616| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.14 r_work: 0.2853 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30014 Z= 0.120 Angle : 0.481 13.871 40756 Z= 0.249 Chirality : 0.041 0.146 4741 Planarity : 0.004 0.047 5356 Dihedral : 6.161 87.301 4342 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Rotamer: Outliers : 1.10 % Allowed : 9.67 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.59 (0.14), residues: 3850 helix: 2.59 (0.12), residues: 1715 sheet: 0.73 (0.22), residues: 532 loop : -0.56 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 88 TYR 0.012 0.001 TYR G 92 PHE 0.026 0.001 PHE E 423 TRP 0.007 0.001 TRP H 63 HIS 0.002 0.001 HIS D 327 Details of bonding type rmsd covalent geometry : bond 0.00269 (30014) covalent geometry : angle 0.48068 (40756) hydrogen bonds : bond 0.04967 ( 1589) hydrogen bonds : angle 4.21734 ( 4602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 ASP cc_start: 0.8088 (t0) cc_final: 0.7599 (m-30) REVERT: A 517 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7717 (p) REVERT: B 1 MET cc_start: 0.5955 (tpt) cc_final: 0.4823 (ptt) REVERT: B 45 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8191 (mm-30) REVERT: B 384 LYS cc_start: 0.8708 (mttp) cc_final: 0.8443 (mttt) REVERT: C 45 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8204 (mm-30) REVERT: C 72 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7946 (mmm160) REVERT: C 388 GLU cc_start: 0.7825 (tt0) cc_final: 0.7486 (mt-10) REVERT: D 27 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7282 (tpm170) REVERT: D 136 GLU cc_start: 0.8186 (tt0) cc_final: 0.7311 (mp0) REVERT: D 288 MET cc_start: 0.8669 (tpp) cc_final: 0.8433 (tpt) REVERT: D 306 MET cc_start: 0.9252 (ttt) cc_final: 0.8972 (ttt) REVERT: D 457 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: D 467 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7318 (tmtm) REVERT: E 426 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7042 (tt0) REVERT: F 381 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: F 398 GLU cc_start: 0.7598 (pt0) cc_final: 0.7260 (mp0) REVERT: F 445 LYS cc_start: 0.7843 (mmtp) cc_final: 0.7338 (mtmt) REVERT: F 454 GLN cc_start: 0.8192 (mm110) cc_final: 0.7464 (mp-120) REVERT: G 108 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6332 (tpp80) REVERT: H 15 ILE cc_start: 0.7040 (mm) cc_final: 0.6564 (pp) REVERT: d 90 GLN cc_start: 0.6571 (tt0) cc_final: 0.6055 (mt0) REVERT: d 104 GLU cc_start: 0.8434 (tp30) cc_final: 0.8100 (tp30) REVERT: d 166 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7441 (mtm180) REVERT: d 265 ARG cc_start: 0.7297 (mtp85) cc_final: 0.7044 (mmm160) outliers start: 34 outliers final: 21 residues processed: 201 average time/residue: 0.7468 time to fit residues: 172.9681 Evaluate side-chains 201 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 387 ILE Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain d residue 166 ARG Chi-restraints excluded: chain d residue 269 SER Chi-restraints excluded: chain d residue 335 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 18 optimal weight: 0.6980 chunk 338 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 251 optimal weight: 0.0050 chunk 192 optimal weight: 0.7980 chunk 125 optimal weight: 0.2980 chunk 122 optimal weight: 0.0970 chunk 329 optimal weight: 10.0000 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 335 ASN G 287 GLN d 381 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085120 restraints weight = 43429.333| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.07 r_work: 0.2903 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30014 Z= 0.091 Angle : 0.445 13.479 40756 Z= 0.231 Chirality : 0.039 0.145 4741 Planarity : 0.003 0.046 5356 Dihedral : 5.892 82.015 4342 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.00 % Allowed : 9.83 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.77 (0.14), residues: 3850 helix: 2.72 (0.13), residues: 1717 sheet: 0.83 (0.22), residues: 530 loop : -0.44 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 105 TYR 0.010 0.001 TYR G 92 PHE 0.020 0.001 PHE E 423 TRP 0.008 0.001 TRP H 62 HIS 0.002 0.000 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00173 (30014) covalent geometry : angle 0.44512 (40756) hydrogen bonds : bond 0.04146 ( 1589) hydrogen bonds : angle 4.04232 ( 4602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8883 (tt) REVERT: A 485 ASP cc_start: 0.7997 (t0) cc_final: 0.7558 (m-30) REVERT: A 517 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7646 (p) REVERT: B 1 MET cc_start: 0.5909 (tpt) cc_final: 0.5414 (OUTLIER) REVERT: B 45 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8190 (mm-30) REVERT: B 83 GLN cc_start: 0.8060 (tt0) cc_final: 0.7428 (tm-30) REVERT: B 384 LYS cc_start: 0.8725 (mttp) cc_final: 0.8473 (mttt) REVERT: B 465 MET cc_start: 0.8167 (mtp) cc_final: 0.7912 (mtm) REVERT: C 72 ARG cc_start: 0.8348 (mtp85) cc_final: 0.7957 (mmm160) REVERT: C 388 GLU cc_start: 0.7832 (tt0) cc_final: 0.7521 (mt-10) REVERT: D 27 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7273 (tpm170) REVERT: D 136 GLU cc_start: 0.8122 (tt0) cc_final: 0.7284 (mp0) REVERT: D 288 MET cc_start: 0.8630 (tpp) cc_final: 0.8408 (tpt) REVERT: D 457 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: D 467 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7328 (tmtm) REVERT: E 426 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7002 (tt0) REVERT: F 381 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: F 398 GLU cc_start: 0.7513 (pt0) cc_final: 0.7217 (mp0) REVERT: F 445 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7232 (mtmt) REVERT: F 454 GLN cc_start: 0.8157 (mm110) cc_final: 0.7452 (mp-120) REVERT: G 108 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6269 (tpp80) REVERT: G 194 LEU cc_start: 0.8398 (mt) cc_final: 0.7657 (tp) REVERT: H 15 ILE cc_start: 0.7009 (mm) cc_final: 0.6564 (pp) REVERT: d 90 GLN cc_start: 0.6530 (tt0) cc_final: 0.6029 (mt0) REVERT: d 104 GLU cc_start: 0.8415 (tp30) cc_final: 0.8092 (tp30) REVERT: d 166 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7376 (mtm180) REVERT: d 265 ARG cc_start: 0.7274 (mtp85) cc_final: 0.7044 (mmm160) outliers start: 31 outliers final: 20 residues processed: 208 average time/residue: 0.7228 time to fit residues: 174.3230 Evaluate side-chains 199 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain d residue 166 ARG Chi-restraints excluded: chain d residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 354 optimal weight: 7.9990 chunk 166 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 373 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 341 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.083330 restraints weight = 43555.665| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.14 r_work: 0.2868 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30014 Z= 0.113 Angle : 0.476 15.908 40756 Z= 0.246 Chirality : 0.041 0.142 4741 Planarity : 0.004 0.046 5356 Dihedral : 5.954 82.998 4342 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.93 % Allowed : 10.12 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.74 (0.14), residues: 3850 helix: 2.69 (0.13), residues: 1716 sheet: 0.85 (0.22), residues: 525 loop : -0.47 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 88 TYR 0.011 0.001 TYR G 92 PHE 0.016 0.001 PHE E 423 TRP 0.006 0.001 TRP A 247 HIS 0.002 0.001 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00252 (30014) covalent geometry : angle 0.47577 (40756) hydrogen bonds : bond 0.04686 ( 1589) hydrogen bonds : angle 4.09955 ( 4602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 ASP cc_start: 0.8049 (t0) cc_final: 0.7580 (m-30) REVERT: A 517 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.7662 (p) REVERT: B 1 MET cc_start: 0.5942 (tpt) cc_final: 0.4884 (ptt) REVERT: B 45 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8173 (mm-30) REVERT: B 384 LYS cc_start: 0.8713 (mttp) cc_final: 0.8452 (mttt) REVERT: C 72 ARG cc_start: 0.8347 (mtp85) cc_final: 0.7940 (mmm160) REVERT: C 388 GLU cc_start: 0.7832 (tt0) cc_final: 0.7514 (mt-10) REVERT: D 27 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7282 (tpm170) REVERT: D 136 GLU cc_start: 0.8119 (tt0) cc_final: 0.7245 (mp0) REVERT: D 288 MET cc_start: 0.8637 (tpp) cc_final: 0.8429 (tpt) REVERT: D 457 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: D 467 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7315 (tmtm) REVERT: E 426 GLN cc_start: 0.8034 (mm-40) cc_final: 0.6984 (tt0) REVERT: F 381 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: F 445 LYS cc_start: 0.7830 (mmtp) cc_final: 0.7325 (mtmt) REVERT: F 454 GLN cc_start: 0.8194 (mm110) cc_final: 0.7469 (mp-120) REVERT: G 108 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6306 (tpp80) REVERT: H 15 ILE cc_start: 0.7042 (mm) cc_final: 0.6570 (pp) REVERT: d 90 GLN cc_start: 0.6532 (tt0) cc_final: 0.6020 (mt0) REVERT: d 104 GLU cc_start: 0.8439 (tp30) cc_final: 0.8109 (tp30) REVERT: d 166 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7379 (mtm180) REVERT: d 265 ARG cc_start: 0.7292 (mtp85) cc_final: 0.7057 (mmm160) outliers start: 29 outliers final: 21 residues processed: 195 average time/residue: 0.8357 time to fit residues: 188.3955 Evaluate side-chains 201 residues out of total 3102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain D residue 471 SER Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 471 SER Chi-restraints excluded: chain F residue 381 GLN Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 108 ARG Chi-restraints excluded: chain G residue 185 ILE Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain d residue 166 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 270 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 361 optimal weight: 5.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.082355 restraints weight = 43872.224| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.15 r_work: 0.2849 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30014 Z= 0.133 Angle : 0.494 15.853 40756 Z= 0.255 Chirality : 0.041 0.185 4741 Planarity : 0.004 0.047 5356 Dihedral : 6.079 85.054 4342 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 1.03 % Allowed : 10.09 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.14 % 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: 1.65 (0.14), residues: 3850 helix: 2.62 (0.12), residues: 1716 sheet: 0.79 (0.22), residues: 532 loop : -0.52 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 88 TYR 0.012 0.001 TYR G 92 PHE 0.015 0.001 PHE E 423 TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS D 327 Details of bonding type rmsd covalent geometry : bond 0.00310 (30014) covalent geometry : angle 0.49372 (40756) hydrogen bonds : bond 0.05035 ( 1589) hydrogen bonds : angle 4.18011 ( 4602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10843.92 seconds wall clock time: 185 minutes 12.20 seconds (11112.20 seconds total)