Starting phenix.real_space_refine on Mon Apr 6 04:03:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cje_45629/04_2026/9cje_45629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cje_45629/04_2026/9cje_45629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cje_45629/04_2026/9cje_45629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cje_45629/04_2026/9cje_45629.map" model { file = "/net/cci-nas-00/data/ceres_data/9cje_45629/04_2026/9cje_45629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cje_45629/04_2026/9cje_45629.cif" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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 Mo 2 10.26 5 Fe 32 7.16 5 S 134 5.16 5 C 9692 2.51 5 N 2570 2.21 5 O 3439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15869 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3036 Classifications: {'peptide': 385} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 366} Chain breaks: 2 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'CLF': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Classifications: {'water': 163} Link IDs: {None: 162} Chain: "B" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Classifications: {'water': 208} Link IDs: {None: 207} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "D" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 195 Classifications: {'water': 195} Link IDs: {None: 194} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 35.132 59.903 97.664 1.00 25.47 S ATOM 1170 SG CYS A 154 52.735 46.202 98.194 1.00 24.87 S ATOM 4549 SG CYS B 95 50.866 43.551 93.955 1.00 35.69 S ATOM 465 SG CYS A 62 47.701 49.171 95.559 1.00 17.26 S ATOM 652 SG CYS A 88 53.479 48.667 92.238 1.00 20.44 S ATOM 652 SG CYS A 88 53.479 48.667 92.238 1.00 20.44 S ATOM 5002 SG CYS B 153 55.879 44.699 94.837 1.00 30.99 S ATOM 4369 SG CYS B 70 53.994 43.474 87.930 1.00 32.80 S ATOM 4549 SG CYS B 95 50.866 43.551 93.955 1.00 35.69 S ATOM 9675 SG CYS C 275 50.735 60.660 21.912 1.00 52.59 S ATOM 8756 SG CYS C 154 31.321 49.942 20.753 1.00 31.24 S ATOM 11759 SG CYS D 95 32.736 46.810 24.706 1.00 47.40 S ATOM 8051 SG CYS C 62 36.871 51.775 23.416 1.00 5.51 S ATOM 8238 SG CYS C 88 30.999 52.139 26.771 1.00 19.84 S ATOM 8238 SG CYS C 88 30.999 52.139 26.771 1.00 19.84 S ATOM 12212 SG CYS D 153 28.005 48.747 23.972 1.00 39.20 S ATOM 11579 SG CYS D 70 29.600 46.774 30.728 1.00 33.73 S ATOM 11759 SG CYS D 95 32.736 46.810 24.706 1.00 47.40 S Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 15869 At special positions: 0 Unit cell: (84.5, 96.85, 124.15, 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) Mo 2 41.97 Fe 32 26.01 S 134 16.00 O 3439 8.00 N 2570 7.00 C 9692 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 650.0 milliseconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 12 sheets defined 58.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.036A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 4.234A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.583A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.106A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.749A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.685A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 4.213A pdb=" N LYS A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.583A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.250A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.550A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 3.993A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.120A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.110A pdb=" N PHE B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.827A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.087A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.261A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.903A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.372A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 85 through 93 removed outlier: 4.607A pdb=" N GLY C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.151A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 158 " --> pdb=" O CYS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.786A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 264 Processing helix chain 'C' and resid 265 through 268 Processing helix chain 'C' and resid 275 through 291 removed outlier: 3.531A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 363 through 370 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.144A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.644A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 81 removed outlier: 3.969A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.024A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.552A pdb=" N PHE D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.830A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 320 through 337 removed outlier: 4.101A pdb=" N TRP D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.221A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.773A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.414A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.183A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.233A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.246A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.570A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.296A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N PHE B 367 " --> pdb=" O PRO B 390 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 removed outlier: 7.005A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.481A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 374 removed outlier: 6.323A pdb=" N LYS C 349 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.434A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.327A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE D 367 " --> pdb=" O PRO D 390 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) 757 hydrogen bonds defined for protein. 2166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.57: 15390 1.57 - 1.92: 171 1.92 - 2.27: 49 2.27 - 2.63: 69 2.63 - 2.98: 18 Bond restraints: 15697 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.983 -0.783 2.00e-02 2.50e+03 1.53e+03 bond pdb="FE2 CLF A 503 " pdb="FE8 CLF A 503 " ideal model delta sigma weight residual 2.200 2.964 -0.764 2.00e-02 2.50e+03 1.46e+03 bond pdb="FE4 CLF A 503 " pdb="FE5 CLF A 503 " ideal model delta sigma weight residual 2.200 2.943 -0.743 2.00e-02 2.50e+03 1.38e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.929 -0.729 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE6 CLF A 503 " pdb="FE7 CLF A 503 " ideal model delta sigma weight residual 2.200 2.850 -0.650 2.00e-02 2.50e+03 1.06e+03 ... (remaining 15692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.83: 21170 6.83 - 13.65: 3 13.65 - 20.48: 2 20.48 - 27.31: 0 27.31 - 34.13: 4 Bond angle restraints: 21179 Sorted by residual: angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.87 34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE4 CLF A 503 " ideal model delta sigma weight residual 90.00 55.87 34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE1 CLF A 503 " ideal model delta sigma weight residual 90.00 56.99 33.01 3.00e+00 1.11e-01 1.21e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 57.14 32.86 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE3 CLF A 503 " ideal model delta sigma weight residual 90.00 107.01 -17.01 3.00e+00 1.11e-01 3.22e+01 ... (remaining 21174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 8415 17.52 - 35.05: 860 35.05 - 52.57: 226 52.57 - 70.09: 64 70.09 - 87.61: 31 Dihedral angle restraints: 9596 sinusoidal: 4136 harmonic: 5460 Sorted by residual: dihedral pdb=" CA ILE A 75 " pdb=" C ILE A 75 " pdb=" N LYS A 76 " pdb=" CA LYS A 76 " ideal model delta harmonic sigma weight residual 180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER D 11 " pdb=" C SER D 11 " pdb=" N TYR D 12 " pdb=" CA TYR D 12 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA SER B 11 " pdb=" C SER B 11 " pdb=" N TYR B 12 " pdb=" CA TYR B 12 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 9593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1437 0.036 - 0.071: 542 0.071 - 0.107: 185 0.107 - 0.143: 57 0.143 - 0.179: 2 Chirality restraints: 2223 Sorted by residual: chirality pdb=" CA ILE C 59 " pdb=" N ILE C 59 " pdb=" C ILE C 59 " pdb=" CB ILE C 59 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA GLN C 191 " pdb=" N GLN C 191 " pdb=" C GLN C 191 " pdb=" CB GLN C 191 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2220 not shown) Planarity restraints: 2714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 57 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C MET C 57 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 57 " -0.021 2.00e-02 2.50e+03 pdb=" N THR C 58 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 58 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C THR C 58 " 0.042 2.00e-02 2.50e+03 pdb=" O THR C 58 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE C 59 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 92 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C SER D 92 " 0.036 2.00e-02 2.50e+03 pdb=" O SER D 92 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN D 93 " -0.012 2.00e-02 2.50e+03 ... (remaining 2711 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 422 2.63 - 3.20: 14652 3.20 - 3.77: 29837 3.77 - 4.33: 42985 4.33 - 4.90: 65432 Nonbonded interactions: 153328 Sorted by model distance: nonbonded pdb="FE FE B 601 " pdb=" O HOH D 790 " model vdw 2.066 2.260 nonbonded pdb="FE FE B 601 " pdb=" O HOH D 765 " model vdw 2.079 2.260 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 601 " model vdw 2.090 2.260 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.104 2.260 nonbonded pdb=" OD2 ASP D 353 " pdb="FE FE D 601 " model vdw 2.132 2.260 ... (remaining 153323 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 'B' selection = (chain 'D' and resid 2 through 601) } 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: 13.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.510 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.024 0.783 15713 Z= 1.263 Angle : 0.729 34.132 21179 Z= 0.340 Chirality : 0.044 0.179 2223 Planarity : 0.004 0.049 2714 Dihedral : 16.250 87.614 6108 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.94 % Rotamer: Outliers : 1.59 % Allowed : 15.51 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1894 helix: 1.31 (0.17), residues: 943 sheet: -0.68 (0.37), residues: 176 loop : -0.27 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 108 TYR 0.017 0.002 TYR B 142 PHE 0.012 0.001 PHE D 201 TRP 0.016 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.02419 (15697) covalent geometry : angle 0.72913 (21179) hydrogen bonds : bond 0.13652 ( 757) hydrogen bonds : angle 6.80765 ( 2166) Misc. bond : bond 0.11813 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.649 Fit side-chains REVERT: B 172 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: C 277 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.4851 (mtt180) outliers start: 26 outliers final: 17 residues processed: 200 average time/residue: 0.7141 time to fit residues: 156.7577 Evaluate side-chains 191 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 376 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN B 268 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN C 90 GLN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128759 restraints weight = 14069.543| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 0.93 r_work: 0.3477 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 15713 Z= 0.178 Angle : 0.718 29.094 21179 Z= 0.341 Chirality : 0.045 0.145 2223 Planarity : 0.004 0.047 2714 Dihedral : 5.632 57.946 2425 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.38 % Allowed : 14.41 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1894 helix: 1.28 (0.17), residues: 960 sheet: -0.67 (0.35), residues: 192 loop : -0.25 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 108 TYR 0.017 0.002 TYR B 142 PHE 0.014 0.002 PHE D 201 TRP 0.016 0.002 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00370 (15697) covalent geometry : angle 0.71839 (21179) hydrogen bonds : bond 0.05073 ( 757) hydrogen bonds : angle 5.79317 ( 2166) Misc. bond : bond 0.09349 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.633 Fit side-chains REVERT: C 287 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.5319 (tp30) REVERT: C 421 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.5763 (mp) outliers start: 39 outliers final: 14 residues processed: 199 average time/residue: 0.7443 time to fit residues: 161.9433 Evaluate side-chains 190 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 53 optimal weight: 0.0020 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN B 268 GLN B 513 GLN C 90 GLN C 195 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131210 restraints weight = 13970.440| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 0.93 r_work: 0.3509 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 15713 Z= 0.140 Angle : 0.677 29.152 21179 Z= 0.315 Chirality : 0.043 0.145 2223 Planarity : 0.004 0.048 2714 Dihedral : 4.826 54.621 2401 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.63 % Allowed : 14.16 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1894 helix: 1.42 (0.17), residues: 958 sheet: -0.70 (0.35), residues: 192 loop : -0.13 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 108 TYR 0.014 0.001 TYR B 88 PHE 0.010 0.001 PHE A 459 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00282 (15697) covalent geometry : angle 0.67732 (21179) hydrogen bonds : bond 0.04296 ( 757) hydrogen bonds : angle 5.51151 ( 2166) Misc. bond : bond 0.07717 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.695 Fit side-chains REVERT: A 168 LYS cc_start: 0.8154 (tttm) cc_final: 0.7631 (mptt) REVERT: A 345 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8116 (mtp180) REVERT: B 172 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: C 287 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.5261 (tp30) REVERT: C 362 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.6511 (m-70) REVERT: D 54 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: D 172 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: D 271 MET cc_start: 0.8535 (ttt) cc_final: 0.8234 (ttm) outliers start: 43 outliers final: 16 residues processed: 209 average time/residue: 0.7424 time to fit residues: 169.6332 Evaluate side-chains 196 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 150 optimal weight: 7.9990 chunk 183 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN B 268 GLN B 513 GLN C 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131963 restraints weight = 13918.633| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 0.93 r_work: 0.3518 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 15713 Z= 0.134 Angle : 0.669 29.162 21179 Z= 0.310 Chirality : 0.043 0.145 2223 Planarity : 0.004 0.049 2714 Dihedral : 4.759 57.464 2401 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.50 % Allowed : 14.53 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 1894 helix: 1.53 (0.17), residues: 948 sheet: -0.73 (0.35), residues: 192 loop : -0.08 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.014 0.001 TYR B 88 PHE 0.010 0.001 PHE A 459 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00270 (15697) covalent geometry : angle 0.66947 (21179) hydrogen bonds : bond 0.04108 ( 757) hydrogen bonds : angle 5.39891 ( 2166) Misc. bond : bond 0.07201 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.654 Fit side-chains REVERT: A 168 LYS cc_start: 0.8158 (tttm) cc_final: 0.7608 (mttt) REVERT: A 345 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8135 (mtp180) REVERT: A 414 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8343 (mtpp) REVERT: A 476 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7667 (tm130) REVERT: B 172 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: C 287 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.5234 (tp30) REVERT: C 300 PHE cc_start: 0.6815 (t80) cc_final: 0.6594 (t80) REVERT: D 172 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: D 211 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7448 (mmmt) REVERT: D 271 MET cc_start: 0.8529 (ttt) cc_final: 0.8258 (ttm) outliers start: 41 outliers final: 17 residues processed: 208 average time/residue: 0.7323 time to fit residues: 166.4911 Evaluate side-chains 192 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 7 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 184 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 268 GLN B 513 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.147118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.129268 restraints weight = 13818.251| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.92 r_work: 0.3484 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 15713 Z= 0.176 Angle : 0.706 29.294 21179 Z= 0.333 Chirality : 0.045 0.146 2223 Planarity : 0.004 0.049 2714 Dihedral : 4.940 56.085 2401 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.20 % Allowed : 15.20 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1894 helix: 1.35 (0.17), residues: 962 sheet: -0.74 (0.35), residues: 192 loop : -0.20 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.017 0.002 TYR B 142 PHE 0.014 0.002 PHE B 201 TRP 0.015 0.002 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00370 (15697) covalent geometry : angle 0.70601 (21179) hydrogen bonds : bond 0.04726 ( 757) hydrogen bonds : angle 5.50697 ( 2166) Misc. bond : bond 0.08577 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.677 Fit side-chains REVERT: A 168 LYS cc_start: 0.8165 (tttm) cc_final: 0.7625 (mttt) REVERT: A 345 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8176 (mtp180) REVERT: B 172 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: C 287 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.5313 (tp30) REVERT: C 300 PHE cc_start: 0.6849 (t80) cc_final: 0.6642 (t80) REVERT: C 334 GLU cc_start: 0.6404 (mm-30) cc_final: 0.5769 (tt0) REVERT: D 172 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: D 211 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7461 (mmmt) REVERT: D 271 MET cc_start: 0.8562 (ttt) cc_final: 0.8253 (ttm) outliers start: 36 outliers final: 20 residues processed: 200 average time/residue: 0.7256 time to fit residues: 158.9411 Evaluate side-chains 195 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 12 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN B 268 GLN B 513 GLN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130627 restraints weight = 13700.902| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 0.92 r_work: 0.3498 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 15713 Z= 0.147 Angle : 0.683 29.209 21179 Z= 0.319 Chirality : 0.044 0.145 2223 Planarity : 0.004 0.049 2714 Dihedral : 4.813 52.195 2401 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.44 % Allowed : 15.26 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1894 helix: 1.42 (0.17), residues: 961 sheet: -0.76 (0.35), residues: 192 loop : -0.18 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.015 0.002 TYR B 142 PHE 0.011 0.001 PHE B 201 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00302 (15697) covalent geometry : angle 0.68309 (21179) hydrogen bonds : bond 0.04341 ( 757) hydrogen bonds : angle 5.42707 ( 2166) Misc. bond : bond 0.07806 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.658 Fit side-chains REVERT: A 168 LYS cc_start: 0.8158 (tttm) cc_final: 0.7621 (mptt) REVERT: A 345 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8170 (mtp180) REVERT: B 172 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: C 287 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.5172 (tp30) REVERT: C 300 PHE cc_start: 0.6787 (t80) cc_final: 0.6578 (t80) REVERT: C 334 GLU cc_start: 0.6371 (mm-30) cc_final: 0.5802 (tt0) REVERT: D 172 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: D 211 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7460 (mmmt) REVERT: D 271 MET cc_start: 0.8555 (ttt) cc_final: 0.8249 (ttm) outliers start: 40 outliers final: 21 residues processed: 204 average time/residue: 0.7413 time to fit residues: 165.5703 Evaluate side-chains 199 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 379 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 84 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN B 268 GLN B 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129413 restraints weight = 13712.954| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 0.91 r_work: 0.3486 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 15713 Z= 0.168 Angle : 0.701 29.285 21179 Z= 0.330 Chirality : 0.045 0.145 2223 Planarity : 0.004 0.049 2714 Dihedral : 4.866 52.472 2401 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 15.45 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1894 helix: 1.36 (0.17), residues: 961 sheet: -0.76 (0.35), residues: 192 loop : -0.22 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.017 0.002 TYR B 142 PHE 0.013 0.002 PHE B 201 TRP 0.015 0.002 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00353 (15697) covalent geometry : angle 0.70107 (21179) hydrogen bonds : bond 0.04639 ( 757) hydrogen bonds : angle 5.48393 ( 2166) Misc. bond : bond 0.08340 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.554 Fit side-chains REVERT: A 168 LYS cc_start: 0.8165 (tttm) cc_final: 0.7626 (mptt) REVERT: A 345 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8179 (mtp180) REVERT: B 172 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: C 287 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.5216 (tp30) REVERT: C 300 PHE cc_start: 0.6795 (t80) cc_final: 0.6581 (t80) REVERT: C 334 GLU cc_start: 0.6393 (mm-30) cc_final: 0.5754 (tt0) REVERT: D 172 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: D 211 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7467 (mmmt) REVERT: D 271 MET cc_start: 0.8550 (ttt) cc_final: 0.8236 (ttm) outliers start: 35 outliers final: 22 residues processed: 199 average time/residue: 0.7175 time to fit residues: 156.2369 Evaluate side-chains 200 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 53 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN B 268 GLN B 513 GLN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129766 restraints weight = 13617.193| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.91 r_work: 0.3487 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 15713 Z= 0.162 Angle : 0.697 29.268 21179 Z= 0.327 Chirality : 0.045 0.146 2223 Planarity : 0.004 0.050 2714 Dihedral : 4.850 52.412 2401 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.95 % Allowed : 15.93 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1894 helix: 1.37 (0.17), residues: 961 sheet: -0.77 (0.35), residues: 193 loop : -0.22 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.016 0.002 TYR B 142 PHE 0.012 0.002 PHE D 201 TRP 0.015 0.002 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00338 (15697) covalent geometry : angle 0.69700 (21179) hydrogen bonds : bond 0.04566 ( 757) hydrogen bonds : angle 5.46835 ( 2166) Misc. bond : bond 0.08157 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.620 Fit side-chains REVERT: A 168 LYS cc_start: 0.8172 (tttm) cc_final: 0.7631 (mptt) REVERT: A 345 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8185 (mtp180) REVERT: B 172 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 287 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.5214 (tp30) REVERT: C 300 PHE cc_start: 0.6792 (t80) cc_final: 0.6579 (t80) REVERT: C 334 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5768 (tt0) REVERT: D 172 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: D 211 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7471 (mmmt) REVERT: D 271 MET cc_start: 0.8539 (ttt) cc_final: 0.8230 (ttm) outliers start: 32 outliers final: 22 residues processed: 197 average time/residue: 0.7241 time to fit residues: 155.9900 Evaluate side-chains 200 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 121 optimal weight: 30.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127791 restraints weight = 13781.284| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 0.92 r_work: 0.3464 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 15713 Z= 0.206 Angle : 0.734 29.403 21179 Z= 0.350 Chirality : 0.047 0.146 2223 Planarity : 0.004 0.050 2714 Dihedral : 5.031 52.860 2401 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.89 % Allowed : 16.06 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1894 helix: 1.25 (0.17), residues: 962 sheet: -0.78 (0.35), residues: 192 loop : -0.27 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 96 TYR 0.018 0.002 TYR B 142 PHE 0.016 0.002 PHE B 201 TRP 0.015 0.002 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00442 (15697) covalent geometry : angle 0.73361 (21179) hydrogen bonds : bond 0.05136 ( 757) hydrogen bonds : angle 5.60234 ( 2166) Misc. bond : bond 0.09350 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.687 Fit side-chains REVERT: A 168 LYS cc_start: 0.8188 (tttm) cc_final: 0.7634 (mttt) REVERT: A 345 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8212 (mtp180) REVERT: B 172 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: C 287 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.5304 (tp30) REVERT: C 334 GLU cc_start: 0.6382 (mm-30) cc_final: 0.5737 (tt0) REVERT: D 172 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: D 211 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7491 (mmmt) REVERT: D 214 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6642 (p0) REVERT: D 271 MET cc_start: 0.8546 (ttt) cc_final: 0.8223 (ttm) outliers start: 31 outliers final: 21 residues processed: 196 average time/residue: 0.7096 time to fit residues: 152.4386 Evaluate side-chains 202 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN B 268 GLN B 513 GLN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130654 restraints weight = 13734.719| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 0.91 r_work: 0.3499 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 15713 Z= 0.141 Angle : 0.684 29.198 21179 Z= 0.320 Chirality : 0.044 0.145 2223 Planarity : 0.004 0.051 2714 Dihedral : 4.828 52.217 2401 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.77 % Allowed : 16.18 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1894 helix: 1.38 (0.17), residues: 961 sheet: -0.78 (0.35), residues: 193 loop : -0.23 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.014 0.001 TYR B 88 PHE 0.011 0.001 PHE A 459 TRP 0.015 0.001 TRP A 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00286 (15697) covalent geometry : angle 0.68383 (21179) hydrogen bonds : bond 0.04289 ( 757) hydrogen bonds : angle 5.43869 ( 2166) Misc. bond : bond 0.07528 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.671 Fit side-chains REVERT: A 168 LYS cc_start: 0.8160 (tttm) cc_final: 0.7624 (mttt) REVERT: A 345 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8173 (mtp180) REVERT: B 172 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: C 300 PHE cc_start: 0.6828 (t80) cc_final: 0.6609 (t80) REVERT: C 334 GLU cc_start: 0.6390 (mm-30) cc_final: 0.5755 (tt0) REVERT: D 172 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: D 211 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7459 (mmmt) REVERT: D 214 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6652 (p0) REVERT: D 271 MET cc_start: 0.8529 (ttt) cc_final: 0.8227 (ttm) outliers start: 29 outliers final: 18 residues processed: 190 average time/residue: 0.7263 time to fit residues: 150.7299 Evaluate side-chains 195 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 179 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 161 optimal weight: 0.4980 chunk 174 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 145 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 476 GLN B 268 GLN B 513 GLN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132463 restraints weight = 13714.719| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 0.90 r_work: 0.3525 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 15713 Z= 0.127 Angle : 0.667 29.147 21179 Z= 0.309 Chirality : 0.043 0.145 2223 Planarity : 0.004 0.050 2714 Dihedral : 4.638 51.217 2400 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.59 % Allowed : 16.42 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1894 helix: 1.48 (0.17), residues: 960 sheet: -0.75 (0.35), residues: 193 loop : -0.16 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 108 TYR 0.013 0.001 TYR B 142 PHE 0.010 0.001 PHE A 459 TRP 0.016 0.001 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00256 (15697) covalent geometry : angle 0.66743 (21179) hydrogen bonds : bond 0.03952 ( 757) hydrogen bonds : angle 5.32957 ( 2166) Misc. bond : bond 0.06682 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6240.83 seconds wall clock time: 107 minutes 25.55 seconds (6445.55 seconds total)