Starting phenix.real_space_refine on Fri Sep 11 16:49:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ram_4780/09_2026/6ram_4780.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ram_4780/09_2026/6ram_4780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ram_4780/09_2026/6ram_4780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ram_4780/09_2026/6ram_4780.map" model { file = "/net/cci-nas-00/data/ceres_data/6ram_4780/09_2026/6ram_4780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ram_4780/09_2026/6ram_4780.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ram_4780/09_2026/6ram_4780.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ram_4780/09_2026/6ram_4780.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6569 2.51 5 N 1797 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10186 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4710 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 24, 'TRANS': 563} Chain: "B" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4519 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 10186 At special positions: 0 Unit cell: (102.315, 87.237, 154.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 5 15.00 Mg 2 11.99 O 1788 8.00 N 1797 7.00 C 6569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 359.3 milliseconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 64.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.966A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 Proline residue: A 24 - end of helix removed outlier: 4.927A pdb=" N LEU A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 45 removed outlier: 3.654A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 72 through 120 removed outlier: 3.705A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.526A pdb=" N LEU A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 155 removed outlier: 3.529A pdb=" N THR A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.905A pdb=" N THR A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.871A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.529A pdb=" N LEU A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 221 removed outlier: 4.457A pdb=" N GLU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 233 through 285 removed outlier: 3.577A pdb=" N GLU A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.619A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 313 through 332 removed outlier: 3.822A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 removed outlier: 3.704A pdb=" N VAL A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.673A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.874A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 484 through 487 removed outlier: 3.656A pdb=" N GLN A 487 " --> pdb=" O LYS A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.690A pdb=" N GLY A 494 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 removed outlier: 3.744A pdb=" N LEU A 507 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 544 removed outlier: 3.928A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.914A pdb=" N ILE A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 598 removed outlier: 3.758A pdb=" N ALA A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.684A pdb=" N TRP B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.651A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 103 removed outlier: 3.565A pdb=" N VAL B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 4.225A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 133 removed outlier: 3.552A pdb=" N LEU B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 removed outlier: 3.811A pdb=" N SER B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 removed outlier: 3.983A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 207 removed outlier: 4.188A pdb=" N GLY B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 217 through 270 removed outlier: 3.881A pdb=" N LEU B 227 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 3.704A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 317 removed outlier: 4.209A pdb=" N LEU B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 4.378A pdb=" N GLY B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.797A pdb=" N LEU B 335 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 removed outlier: 3.602A pdb=" N LEU B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.568A pdb=" N ARG B 404 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.882A pdb=" N GLU B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 460 Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.731A pdb=" N GLU B 465 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 4.276A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 520 Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.788A pdb=" N LEU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.511A pdb=" N GLN B 561 " --> pdb=" O SER B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 removed outlier: 3.751A pdb=" N LEU B 572 " --> pdb=" O GLU B 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 379 removed outlier: 6.144A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 353 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 379 removed outlier: 6.144A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A 416 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL A 358 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ARG A 414 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.308A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LEU A 566 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 577 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU A 575 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 449 removed outlier: 3.532A pdb=" N GLY A 448 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 361 removed outlier: 6.434A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 343 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 344 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 392 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.496A pdb=" N GLY B 415 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP B 499 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 417 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 541 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 552 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP B 546 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE B 550 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.659A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.529A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1692 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: 1.68 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1611 1.31 - 1.44: 3256 1.44 - 1.57: 5474 1.57 - 1.70: 13 1.70 - 1.83: 45 Bond restraints: 10399 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.327 0.060 1.00e-02 1.00e+04 3.54e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.321 0.053 1.00e-02 1.00e+04 2.84e+01 bond pdb=" CA GLY B 368 " pdb=" C GLY B 368 " ideal model delta sigma weight residual 1.519 1.484 0.035 7.00e-03 2.04e+04 2.44e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.457 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 10394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 13684 4.78 - 9.55: 406 9.55 - 14.33: 16 14.33 - 19.11: 0 19.11 - 23.88: 2 Bond angle restraints: 14108 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 115.99 23.88 1.00e+00 1.00e+00 5.70e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 114.66 22.17 1.00e+00 1.00e+00 4.92e+02 angle pdb=" N VAL B 241 " pdb=" CA VAL B 241 " pdb=" C VAL B 241 " ideal model delta sigma weight residual 111.62 101.60 10.02 7.90e-01 1.60e+00 1.61e+02 angle pdb=" N SER B 558 " pdb=" CA SER B 558 " pdb=" C SER B 558 " ideal model delta sigma weight residual 111.36 100.23 11.13 1.09e+00 8.42e-01 1.04e+02 angle pdb=" N ILE B 473 " pdb=" CA ILE B 473 " pdb=" C ILE B 473 " ideal model delta sigma weight residual 113.53 103.64 9.89 9.80e-01 1.04e+00 1.02e+02 ... (remaining 14103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.89: 5889 18.89 - 37.78: 194 37.78 - 56.66: 45 56.66 - 75.55: 24 75.55 - 94.44: 6 Dihedral angle restraints: 6158 sinusoidal: 2496 harmonic: 3662 Sorted by residual: dihedral pdb=" N ASP B 349 " pdb=" C ASP B 349 " pdb=" CA ASP B 349 " pdb=" CB ASP B 349 " ideal model delta harmonic sigma weight residual 122.80 135.65 -12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -154.44 94.44 1 2.00e+01 2.50e-03 2.59e+01 dihedral pdb=" N GLU B 438 " pdb=" C GLU B 438 " pdb=" CA GLU B 438 " pdb=" CB GLU B 438 " ideal model delta harmonic sigma weight residual 122.80 110.37 12.43 0 2.50e+00 1.60e-01 2.47e+01 ... (remaining 6155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1078 0.103 - 0.205: 399 0.205 - 0.308: 93 0.308 - 0.410: 25 0.410 - 0.513: 12 Chirality restraints: 1607 Sorted by residual: chirality pdb=" CA ASN B 123 " pdb=" N ASN B 123 " pdb=" C ASN B 123 " pdb=" CB ASN B 123 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CA GLU A 533 " pdb=" N GLU A 533 " pdb=" C GLU A 533 " pdb=" CB GLU A 533 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CA GLN A 441 " pdb=" N GLN A 441 " pdb=" C GLN A 441 " pdb=" CB GLN A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 1604 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 223 " 0.051 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP B 223 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP B 223 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 223 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 223 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 223 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 223 " -0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 223 " 0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 223 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 223 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 52 " 0.053 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP A 52 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 52 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 52 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 52 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 52 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 52 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 52 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 52 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 52 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 216 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C LEU B 216 " 0.068 2.00e-02 2.50e+03 pdb=" O LEU B 216 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU B 217 " -0.023 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 459 2.71 - 3.26: 10007 3.26 - 3.80: 15369 3.80 - 4.35: 20680 4.35 - 4.90: 33370 Nonbonded interactions: 79885 Sorted by model distance: nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 702 " model vdw 2.162 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.173 2.170 nonbonded pdb=" OE1 GLN A 441 " pdb="MG MG A 702 " model vdw 2.233 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.273 2.170 nonbonded pdb=" O1G ATP B 601 " pdb="MG MG B 602 " model vdw 2.316 2.170 ... (remaining 79880 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.016 0.071 10401 Z= 1.142 Angle : 1.964 23.885 14112 Z= 1.407 Chirality : 0.119 0.513 1607 Planarity : 0.012 0.082 1784 Dihedral : 11.561 94.441 3808 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.82 % Favored : 96.94 % Rotamer: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.95 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.20), residues: 1275 helix: -1.94 (0.16), residues: 745 sheet: -0.77 (0.42), residues: 132 loop : -1.78 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 229 TYR 0.049 0.006 TYR A 277 PHE 0.044 0.007 PHE B 313 TRP 0.053 0.008 TRP A 52 HIS 0.006 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.01648 / 1.14 (10399) covalent geometry : angle 1.96419 / 1.41 (14108) SS BOND : bond 0.02220 / 1.06 ( 2) SS BOND : angle 2.01736 / 1.12 ( 4) hydrogen bonds : bond 0.24935 / 16.21 ( 575) hydrogen bonds : angle 8.57617 / 6.06 ( 1692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ILE cc_start: 0.9395 (mm) cc_final: 0.9152 (mm) REVERT: A 160 PHE cc_start: 0.7924 (m-80) cc_final: 0.7686 (m-80) REVERT: A 303 LEU cc_start: 0.9286 (tp) cc_final: 0.9056 (tp) REVERT: A 309 ASP cc_start: 0.8721 (t0) cc_final: 0.8382 (t70) REVERT: A 321 MET cc_start: 0.8433 (tpt) cc_final: 0.8182 (tpt) REVERT: A 359 TRP cc_start: 0.7903 (m100) cc_final: 0.6883 (m100) REVERT: A 372 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7913 (tptm) REVERT: A 376 LEU cc_start: 0.8173 (mp) cc_final: 0.7886 (mm) REVERT: A 391 LEU cc_start: 0.9224 (mp) cc_final: 0.8647 (tt) REVERT: A 503 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8161 (tp40) REVERT: A 538 GLU cc_start: 0.8616 (tt0) cc_final: 0.8292 (tp30) REVERT: A 554 HIS cc_start: 0.6726 (m90) cc_final: 0.5869 (m-70) REVERT: B 21 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7516 (ptm160) REVERT: B 125 ASP cc_start: 0.6470 (m-30) cc_final: 0.6154 (m-30) REVERT: B 191 GLN cc_start: 0.8573 (tp40) cc_final: 0.8209 (tm-30) REVERT: B 282 ASN cc_start: 0.9411 (t0) cc_final: 0.9014 (t0) REVERT: B 299 MET cc_start: 0.8777 (mmm) cc_final: 0.8476 (mmp) REVERT: B 359 LEU cc_start: 0.8936 (tp) cc_final: 0.8701 (tt) REVERT: B 365 MET cc_start: 0.7840 (ttp) cc_final: 0.7448 (tmm) REVERT: B 505 VAL cc_start: 0.9116 (t) cc_final: 0.8908 (p) REVERT: C 90 ASP cc_start: 0.7806 (m-30) cc_final: 0.7139 (m-30) outliers start: 1 outliers final: 0 residues processed: 328 average time/residue: 0.1383 time to fit residues: 59.4682 Evaluate side-chains 194 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 120 ASN B 123 ASN C 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.100039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080638 restraints weight = 25782.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083492 restraints weight = 13686.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085435 restraints weight = 8882.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086763 restraints weight = 6590.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087672 restraints weight = 5343.743| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10401 Z= 0.151 Angle : 0.703 9.804 14112 Z= 0.356 Chirality : 0.042 0.163 1607 Planarity : 0.006 0.071 1784 Dihedral : 6.119 83.902 1454 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.24 % Allowed : 11.53 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.22), residues: 1275 helix: -0.43 (0.18), residues: 770 sheet: -0.45 (0.45), residues: 121 loop : -1.41 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 569 TYR 0.020 0.002 TYR A 589 PHE 0.023 0.002 PHE A 88 TRP 0.030 0.002 TRP B 290 HIS 0.005 0.002 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10399) covalent geometry : angle 0.70324 / 0.36 (14108) SS BOND : bond 0.01012 / 0.48 ( 2) SS BOND : angle 1.18522 / 0.59 ( 4) hydrogen bonds : bond 0.05150 / 3.38 ( 575) hydrogen bonds : angle 4.71007 / 3.39 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9230 (mt) cc_final: 0.8775 (tt) REVERT: A 40 THR cc_start: 0.9138 (m) cc_final: 0.8817 (p) REVERT: A 94 GLU cc_start: 0.7944 (tp30) cc_final: 0.7605 (tp30) REVERT: A 118 MET cc_start: 0.9001 (mmp) cc_final: 0.8366 (mmp) REVERT: A 305 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8151 (tp40) REVERT: A 309 ASP cc_start: 0.8269 (t0) cc_final: 0.7890 (t0) REVERT: A 359 TRP cc_start: 0.7952 (m100) cc_final: 0.7384 (m100) REVERT: A 444 PHE cc_start: 0.7215 (t80) cc_final: 0.6091 (t80) REVERT: A 569 ARG cc_start: 0.7547 (mtt90) cc_final: 0.7229 (mtt90) REVERT: B 21 ARG cc_start: 0.8054 (ttp-110) cc_final: 0.7766 (ptt90) REVERT: B 132 MET cc_start: 0.8956 (tmm) cc_final: 0.8486 (tmm) REVERT: B 281 PHE cc_start: 0.9059 (t80) cc_final: 0.8410 (t80) REVERT: B 282 ASN cc_start: 0.8969 (t0) cc_final: 0.8765 (t0) REVERT: B 299 MET cc_start: 0.8734 (mmm) cc_final: 0.8422 (mmp) REVERT: B 316 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 365 MET cc_start: 0.7994 (ttp) cc_final: 0.7683 (tmm) REVERT: B 412 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8844 (mttm) REVERT: C 51 ILE cc_start: 0.8863 (tp) cc_final: 0.8611 (tp) REVERT: C 84 ASN cc_start: 0.8516 (m-40) cc_final: 0.7929 (p0) REVERT: C 86 LEU cc_start: 0.8827 (mt) cc_final: 0.8209 (mt) outliers start: 34 outliers final: 13 residues processed: 244 average time/residue: 0.1042 time to fit residues: 35.4176 Evaluate side-chains 182 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 84 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.094464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075278 restraints weight = 26224.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.077861 restraints weight = 14351.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079637 restraints weight = 9548.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.080865 restraints weight = 7199.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.081728 restraints weight = 5903.170| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10401 Z= 0.236 Angle : 0.746 8.924 14112 Z= 0.369 Chirality : 0.044 0.222 1607 Planarity : 0.005 0.043 1784 Dihedral : 5.743 84.453 1450 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.10 % Allowed : 13.44 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.22), residues: 1275 helix: 0.12 (0.18), residues: 772 sheet: -0.24 (0.47), residues: 118 loop : -1.29 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 67 TYR 0.020 0.002 TYR B 92 PHE 0.023 0.002 PHE A 444 TRP 0.028 0.002 TRP B 446 HIS 0.005 0.002 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.24 (10399) covalent geometry : angle 0.74539 / 0.37 (14108) SS BOND : bond 0.00701 / 0.34 ( 2) SS BOND : angle 1.63885 / 1.28 ( 4) hydrogen bonds : bond 0.05014 / 3.23 ( 575) hydrogen bonds : angle 4.63239 / 3.31 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9222 (m) cc_final: 0.8937 (p) REVERT: A 72 LEU cc_start: 0.7986 (mm) cc_final: 0.7651 (mm) REVERT: A 94 GLU cc_start: 0.7991 (tp30) cc_final: 0.7626 (tp30) REVERT: A 140 ASP cc_start: 0.7013 (m-30) cc_final: 0.6403 (m-30) REVERT: A 145 ASN cc_start: 0.8735 (m-40) cc_final: 0.8151 (m-40) REVERT: A 359 TRP cc_start: 0.8095 (m100) cc_final: 0.7327 (m100) REVERT: A 417 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 569 ARG cc_start: 0.7443 (mtt90) cc_final: 0.7237 (mtt180) REVERT: B 38 PHE cc_start: 0.8806 (t80) cc_final: 0.8594 (t80) REVERT: B 132 MET cc_start: 0.9134 (tmm) cc_final: 0.8672 (tmm) REVERT: B 154 MET cc_start: 0.8680 (mmm) cc_final: 0.8317 (mmm) REVERT: B 255 PHE cc_start: 0.8812 (t80) cc_final: 0.8590 (t80) REVERT: B 282 ASN cc_start: 0.9123 (t0) cc_final: 0.8830 (t0) REVERT: B 316 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8635 (mt) REVERT: C 45 ARG cc_start: 0.8386 (mtm110) cc_final: 0.7917 (mtm110) outliers start: 43 outliers final: 21 residues processed: 211 average time/residue: 0.1129 time to fit residues: 32.6847 Evaluate side-chains 173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 117 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN A 243 ASN B 280 GLN B 287 GLN B 419 GLN ** C 82 GLN ** 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 = 0.3568 r_free = 0.3568 target = 0.096244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077051 restraints weight = 26204.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079838 restraints weight = 13903.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081726 restraints weight = 9096.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082930 restraints weight = 6782.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083884 restraints weight = 5566.426| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10401 Z= 0.129 Angle : 0.656 8.565 14112 Z= 0.317 Chirality : 0.040 0.160 1607 Planarity : 0.004 0.039 1784 Dihedral : 5.411 84.040 1450 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.86 % Allowed : 17.54 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1275 helix: 0.58 (0.18), residues: 782 sheet: -0.19 (0.47), residues: 119 loop : -1.18 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 569 TYR 0.027 0.001 TYR C 113 PHE 0.032 0.001 PHE A 15 TRP 0.022 0.002 TRP B 290 HIS 0.004 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10399) covalent geometry : angle 0.65526 / 0.32 (14108) SS BOND : bond 0.00330 / 0.16 ( 2) SS BOND : angle 1.40842 / 0.75 ( 4) hydrogen bonds : bond 0.04150 / 2.72 ( 575) hydrogen bonds : angle 4.23388 / 3.03 ( 1692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9201 (m) cc_final: 0.8916 (p) REVERT: A 72 LEU cc_start: 0.7842 (mm) cc_final: 0.7540 (mm) REVERT: A 94 GLU cc_start: 0.7968 (tp30) cc_final: 0.7653 (tp30) REVERT: A 140 ASP cc_start: 0.6869 (m-30) cc_final: 0.6318 (m-30) REVERT: A 145 ASN cc_start: 0.8665 (m-40) cc_final: 0.8047 (m110) REVERT: A 359 TRP cc_start: 0.8116 (m100) cc_final: 0.7344 (m100) REVERT: A 365 LYS cc_start: 0.8538 (ttmt) cc_final: 0.7971 (ttmt) REVERT: A 391 LEU cc_start: 0.9024 (mp) cc_final: 0.8751 (mt) REVERT: A 417 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8735 (p) REVERT: B 112 LYS cc_start: 0.8718 (mmmt) cc_final: 0.7718 (mttp) REVERT: B 132 MET cc_start: 0.9113 (tmm) cc_final: 0.8694 (tmm) REVERT: B 154 MET cc_start: 0.8665 (mmm) cc_final: 0.7992 (mmm) REVERT: B 282 ASN cc_start: 0.9036 (t0) cc_final: 0.8706 (t0) REVERT: B 365 MET cc_start: 0.8350 (tmm) cc_final: 0.8144 (tmm) REVERT: C 45 ARG cc_start: 0.8467 (mtm110) cc_final: 0.8241 (mtm110) REVERT: C 65 LYS cc_start: 0.8927 (pttp) cc_final: 0.8472 (pttm) REVERT: C 76 LYS cc_start: 0.8966 (tppt) cc_final: 0.8675 (tptp) outliers start: 30 outliers final: 15 residues processed: 191 average time/residue: 0.1125 time to fit residues: 29.8637 Evaluate side-chains 172 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.093439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074531 restraints weight = 26187.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077189 restraints weight = 13979.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079023 restraints weight = 9188.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080209 restraints weight = 6874.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081097 restraints weight = 5646.652| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10401 Z= 0.188 Angle : 0.675 7.876 14112 Z= 0.330 Chirality : 0.041 0.158 1607 Planarity : 0.004 0.048 1784 Dihedral : 5.383 82.055 1450 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.72 % Allowed : 17.45 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.23), residues: 1275 helix: 0.77 (0.19), residues: 780 sheet: -0.10 (0.46), residues: 128 loop : -1.21 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 569 TYR 0.025 0.001 TYR B 92 PHE 0.029 0.001 PHE A 15 TRP 0.011 0.001 TRP A 359 HIS 0.005 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (10399) covalent geometry : angle 0.67469 / 0.33 (14108) SS BOND : bond 0.00396 / 0.19 ( 2) SS BOND : angle 1.56332 / 0.80 ( 4) hydrogen bonds : bond 0.04308 / 2.80 ( 575) hydrogen bonds : angle 4.28500 / 3.06 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9213 (m) cc_final: 0.8951 (p) REVERT: A 94 GLU cc_start: 0.7972 (tp30) cc_final: 0.7613 (tp30) REVERT: A 140 ASP cc_start: 0.6967 (m-30) cc_final: 0.6467 (m-30) REVERT: A 145 ASN cc_start: 0.8729 (m-40) cc_final: 0.7983 (m-40) REVERT: A 391 LEU cc_start: 0.9011 (mp) cc_final: 0.8720 (mt) REVERT: B 130 ARG cc_start: 0.8325 (tmm-80) cc_final: 0.7885 (tmm-80) REVERT: B 132 MET cc_start: 0.9104 (tmm) cc_final: 0.8420 (tmm) REVERT: B 154 MET cc_start: 0.8715 (mmm) cc_final: 0.8121 (mmm) REVERT: B 290 TRP cc_start: 0.8104 (t60) cc_final: 0.7859 (t60) REVERT: B 365 MET cc_start: 0.8369 (tmm) cc_final: 0.8070 (tmm) REVERT: C 13 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7234 (tp40) REVERT: C 39 GLN cc_start: 0.7398 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 65 LYS cc_start: 0.8975 (pttp) cc_final: 0.8638 (pttm) REVERT: C 107 ARG cc_start: 0.7980 (tpp80) cc_final: 0.7737 (ttt90) outliers start: 39 outliers final: 23 residues processed: 190 average time/residue: 0.1041 time to fit residues: 27.9389 Evaluate side-chains 172 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 37 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 0.0370 chunk 40 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN A 308 GLN B 246 HIS B 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.096134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077193 restraints weight = 26141.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079968 restraints weight = 13704.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.081866 restraints weight = 8930.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083151 restraints weight = 6649.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084023 restraints weight = 5418.229| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10401 Z= 0.121 Angle : 0.642 8.491 14112 Z= 0.309 Chirality : 0.040 0.152 1607 Planarity : 0.004 0.039 1784 Dihedral : 5.135 78.437 1450 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.38 % Allowed : 18.88 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1275 helix: 1.03 (0.19), residues: 781 sheet: 0.06 (0.46), residues: 134 loop : -1.25 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 38 TYR 0.023 0.001 TYR B 92 PHE 0.023 0.001 PHE A 15 TRP 0.009 0.001 TRP B 14 HIS 0.004 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10399) covalent geometry : angle 0.64179 / 0.31 (14108) SS BOND : bond 0.00132 / 0.06 ( 2) SS BOND : angle 1.06618 / 0.60 ( 4) hydrogen bonds : bond 0.03822 / 2.52 ( 575) hydrogen bonds : angle 4.14607 / 2.96 ( 1692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9226 (m) cc_final: 0.8945 (p) REVERT: A 94 GLU cc_start: 0.7965 (tp30) cc_final: 0.7588 (tp30) REVERT: A 140 ASP cc_start: 0.7041 (m-30) cc_final: 0.6540 (m-30) REVERT: A 145 ASN cc_start: 0.8648 (m-40) cc_final: 0.8248 (m-40) REVERT: A 391 LEU cc_start: 0.8994 (mp) cc_final: 0.8710 (mt) REVERT: A 493 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7413 (tpp-160) REVERT: B 40 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8012 (tt) REVERT: B 112 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8122 (mttp) REVERT: B 130 ARG cc_start: 0.8253 (tmm-80) cc_final: 0.7842 (tmm-80) REVERT: B 132 MET cc_start: 0.9125 (tmm) cc_final: 0.8485 (tmm) REVERT: B 154 MET cc_start: 0.8661 (mmm) cc_final: 0.8103 (mmm) REVERT: B 253 MET cc_start: 0.8637 (mmm) cc_final: 0.8334 (mmp) REVERT: B 281 PHE cc_start: 0.8842 (t80) cc_final: 0.7566 (t80) REVERT: B 282 ASN cc_start: 0.8671 (t0) cc_final: 0.8361 (t0) REVERT: B 365 MET cc_start: 0.8309 (tmm) cc_final: 0.7971 (tmm) REVERT: C 65 LYS cc_start: 0.8939 (pttp) cc_final: 0.8611 (pttm) REVERT: C 107 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7670 (ttt90) outliers start: 25 outliers final: 17 residues processed: 191 average time/residue: 0.1055 time to fit residues: 28.3450 Evaluate side-chains 170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 34 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077176 restraints weight = 26042.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079921 restraints weight = 13724.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081787 restraints weight = 8945.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083049 restraints weight = 6686.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083888 restraints weight = 5462.131| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10401 Z= 0.124 Angle : 0.645 9.787 14112 Z= 0.311 Chirality : 0.040 0.175 1607 Planarity : 0.004 0.039 1784 Dihedral : 5.014 77.305 1450 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.96 % Allowed : 19.26 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1275 helix: 1.10 (0.19), residues: 788 sheet: 0.16 (0.46), residues: 132 loop : -1.26 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 351 TYR 0.017 0.001 TYR B 16 PHE 0.018 0.001 PHE A 15 TRP 0.011 0.001 TRP B 290 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10399) covalent geometry : angle 0.64491 / 0.31 (14108) SS BOND : bond 0.00154 / 0.07 ( 2) SS BOND : angle 1.28723 / 0.67 ( 4) hydrogen bonds : bond 0.03756 / 2.45 ( 575) hydrogen bonds : angle 4.08797 / 2.91 ( 1692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9246 (m) cc_final: 0.8971 (p) REVERT: A 94 GLU cc_start: 0.7910 (tp30) cc_final: 0.7566 (tp30) REVERT: A 140 ASP cc_start: 0.7013 (m-30) cc_final: 0.6540 (m-30) REVERT: A 391 LEU cc_start: 0.8995 (mp) cc_final: 0.8720 (mt) REVERT: A 441 GLN cc_start: 0.7973 (tt0) cc_final: 0.7731 (tp-100) REVERT: A 492 GLU cc_start: 0.8042 (pt0) cc_final: 0.7720 (pm20) REVERT: B 40 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 112 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8179 (mttp) REVERT: B 130 ARG cc_start: 0.8395 (tmm-80) cc_final: 0.7894 (tmm-80) REVERT: B 132 MET cc_start: 0.9139 (tmm) cc_final: 0.8488 (tmm) REVERT: B 154 MET cc_start: 0.8629 (mmm) cc_final: 0.8100 (mmm) REVERT: B 253 MET cc_start: 0.8640 (mmm) cc_final: 0.8392 (mmp) REVERT: B 281 PHE cc_start: 0.8789 (t80) cc_final: 0.7606 (t80) REVERT: B 282 ASN cc_start: 0.8670 (t0) cc_final: 0.8394 (t0) REVERT: B 365 MET cc_start: 0.8294 (tmm) cc_final: 0.7916 (tmm) REVERT: C 65 LYS cc_start: 0.8948 (pttp) cc_final: 0.8661 (pttm) REVERT: C 107 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7634 (ttt90) outliers start: 31 outliers final: 21 residues processed: 188 average time/residue: 0.1037 time to fit residues: 27.3585 Evaluate side-chains 175 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 243 ASN Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 0.0170 chunk 51 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN A 308 GLN B 191 GLN B 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.075962 restraints weight = 26084.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078620 restraints weight = 14008.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080448 restraints weight = 9245.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081697 restraints weight = 6961.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082518 restraints weight = 5705.885| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10401 Z= 0.147 Angle : 0.663 10.686 14112 Z= 0.319 Chirality : 0.041 0.154 1607 Planarity : 0.004 0.053 1784 Dihedral : 5.007 77.385 1450 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.15 % Allowed : 19.83 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1275 helix: 1.15 (0.19), residues: 788 sheet: 0.07 (0.45), residues: 134 loop : -1.27 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 45 TYR 0.021 0.001 TYR B 16 PHE 0.011 0.001 PHE A 50 TRP 0.012 0.001 TRP C 36 HIS 0.004 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10399) covalent geometry : angle 0.66273 / 0.32 (14108) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 1.29798 / 0.68 ( 4) hydrogen bonds : bond 0.03874 / 2.52 ( 575) hydrogen bonds : angle 4.09586 / 2.91 ( 1692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9256 (m) cc_final: 0.8986 (p) REVERT: A 94 GLU cc_start: 0.7933 (tp30) cc_final: 0.7578 (tp30) REVERT: A 140 ASP cc_start: 0.7072 (m-30) cc_final: 0.6522 (m-30) REVERT: A 391 LEU cc_start: 0.9033 (mp) cc_final: 0.8775 (mt) REVERT: A 441 GLN cc_start: 0.7979 (tt0) cc_final: 0.7737 (tp-100) REVERT: A 492 GLU cc_start: 0.8094 (pt0) cc_final: 0.7734 (pm20) REVERT: A 595 LEU cc_start: 0.8695 (mt) cc_final: 0.8334 (pp) REVERT: B 38 PHE cc_start: 0.8907 (t80) cc_final: 0.8687 (t80) REVERT: B 40 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8284 (tt) REVERT: B 130 ARG cc_start: 0.8415 (tmm-80) cc_final: 0.7905 (tmm-80) REVERT: B 132 MET cc_start: 0.9136 (tmm) cc_final: 0.8525 (tmm) REVERT: B 154 MET cc_start: 0.8662 (mmm) cc_final: 0.8307 (mmm) REVERT: B 253 MET cc_start: 0.8669 (mmm) cc_final: 0.8443 (mmp) REVERT: B 282 ASN cc_start: 0.8668 (t0) cc_final: 0.8368 (t0) REVERT: B 290 TRP cc_start: 0.8126 (t60) cc_final: 0.7879 (t60) REVERT: B 365 MET cc_start: 0.8313 (tmm) cc_final: 0.7886 (tmm) REVERT: C 45 ARG cc_start: 0.8274 (mtm110) cc_final: 0.7791 (mtm110) REVERT: C 65 LYS cc_start: 0.8968 (pttp) cc_final: 0.8710 (pttm) REVERT: C 89 GLU cc_start: 0.7613 (pp20) cc_final: 0.7406 (pp20) REVERT: C 107 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7542 (ttt90) outliers start: 33 outliers final: 25 residues processed: 177 average time/residue: 0.1046 time to fit residues: 26.1894 Evaluate side-chains 175 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN A 308 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.096992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078033 restraints weight = 25906.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080803 restraints weight = 13571.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082664 restraints weight = 8800.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083947 restraints weight = 6545.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084709 restraints weight = 5319.413| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10401 Z= 0.116 Angle : 0.662 10.225 14112 Z= 0.314 Chirality : 0.039 0.158 1607 Planarity : 0.004 0.040 1784 Dihedral : 4.896 75.705 1450 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.57 % Allowed : 20.40 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.24), residues: 1275 helix: 1.21 (0.19), residues: 788 sheet: 0.11 (0.45), residues: 134 loop : -1.20 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 38 TYR 0.022 0.001 TYR B 92 PHE 0.025 0.001 PHE A 15 TRP 0.008 0.001 TRP C 36 HIS 0.003 0.001 HIS C 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10399) covalent geometry : angle 0.66234 / 0.31 (14108) SS BOND : bond 0.00171 / 0.08 ( 2) SS BOND : angle 0.99346 / 0.47 ( 4) hydrogen bonds : bond 0.03659 / 2.41 ( 575) hydrogen bonds : angle 3.98224 / 2.83 ( 1692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9243 (m) cc_final: 0.8963 (p) REVERT: A 94 GLU cc_start: 0.7916 (tp30) cc_final: 0.7563 (tp30) REVERT: A 140 ASP cc_start: 0.7029 (m-30) cc_final: 0.6488 (m-30) REVERT: A 391 LEU cc_start: 0.9017 (mp) cc_final: 0.8764 (mt) REVERT: A 441 GLN cc_start: 0.7959 (tt0) cc_final: 0.7725 (tp-100) REVERT: A 492 GLU cc_start: 0.8061 (pt0) cc_final: 0.7714 (pm20) REVERT: A 595 LEU cc_start: 0.8601 (mt) cc_final: 0.8235 (pp) REVERT: B 38 PHE cc_start: 0.8881 (t80) cc_final: 0.8656 (t80) REVERT: B 40 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8146 (tt) REVERT: B 130 ARG cc_start: 0.8411 (tmm-80) cc_final: 0.7960 (tmm-80) REVERT: B 132 MET cc_start: 0.9156 (tmm) cc_final: 0.8552 (tmm) REVERT: B 154 MET cc_start: 0.8603 (mmm) cc_final: 0.8190 (mmm) REVERT: B 290 TRP cc_start: 0.8096 (t60) cc_final: 0.7679 (t60) REVERT: B 365 MET cc_start: 0.8262 (tmm) cc_final: 0.7852 (tmm) REVERT: C 45 ARG cc_start: 0.8303 (mtm110) cc_final: 0.7825 (mtm110) REVERT: C 65 LYS cc_start: 0.8907 (pttp) cc_final: 0.8678 (pttm) REVERT: C 83 MET cc_start: 0.9280 (mpp) cc_final: 0.9022 (mpp) REVERT: C 95 TYR cc_start: 0.8591 (m-80) cc_final: 0.8285 (m-80) REVERT: C 107 ARG cc_start: 0.7818 (tpp80) cc_final: 0.7511 (ttt90) outliers start: 27 outliers final: 21 residues processed: 180 average time/residue: 0.1109 time to fit residues: 27.7543 Evaluate side-chains 178 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN A 308 GLN B 191 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078870 restraints weight = 25631.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081642 restraints weight = 13544.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083518 restraints weight = 8823.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084783 restraints weight = 6572.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085642 restraints weight = 5360.036| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10401 Z= 0.120 Angle : 0.687 11.104 14112 Z= 0.326 Chirality : 0.040 0.154 1607 Planarity : 0.004 0.040 1784 Dihedral : 4.832 75.052 1450 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.10 % Allowed : 21.16 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1275 helix: 1.25 (0.19), residues: 789 sheet: 0.31 (0.47), residues: 127 loop : -1.17 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 38 TYR 0.019 0.001 TYR B 92 PHE 0.020 0.001 PHE A 50 TRP 0.009 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10399) covalent geometry : angle 0.68703 / 0.33 (14108) SS BOND : bond 0.00184 / 0.09 ( 2) SS BOND : angle 1.09300 / 0.53 ( 4) hydrogen bonds : bond 0.03605 / 2.39 ( 575) hydrogen bonds : angle 3.97223 / 2.82 ( 1692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9243 (m) cc_final: 0.8964 (p) REVERT: A 94 GLU cc_start: 0.8056 (tp30) cc_final: 0.7683 (tp30) REVERT: A 140 ASP cc_start: 0.7055 (m-30) cc_final: 0.6664 (m-30) REVERT: A 391 LEU cc_start: 0.9020 (mp) cc_final: 0.8765 (mt) REVERT: A 441 GLN cc_start: 0.7915 (tt0) cc_final: 0.7666 (tp-100) REVERT: A 492 GLU cc_start: 0.8039 (pt0) cc_final: 0.7724 (pm20) REVERT: B 40 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8036 (tt) REVERT: B 130 ARG cc_start: 0.8489 (tmm-80) cc_final: 0.7974 (tmm-80) REVERT: B 132 MET cc_start: 0.9173 (tmm) cc_final: 0.8529 (tmm) REVERT: B 154 MET cc_start: 0.8608 (mmm) cc_final: 0.8223 (mmm) REVERT: B 290 TRP cc_start: 0.8163 (t60) cc_final: 0.7761 (t60) REVERT: B 365 MET cc_start: 0.8261 (tmm) cc_final: 0.7859 (tmm) REVERT: B 481 GLN cc_start: 0.8739 (mp10) cc_final: 0.8432 (mp10) REVERT: C 45 ARG cc_start: 0.8270 (mtm110) cc_final: 0.7815 (mtm110) REVERT: C 65 LYS cc_start: 0.8947 (pttp) cc_final: 0.8703 (pttm) REVERT: C 83 MET cc_start: 0.9273 (mpp) cc_final: 0.9024 (mpp) REVERT: C 95 TYR cc_start: 0.8592 (m-80) cc_final: 0.8278 (m-80) REVERT: C 107 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7466 (ttt90) outliers start: 22 outliers final: 20 residues processed: 178 average time/residue: 0.1054 time to fit residues: 26.4272 Evaluate side-chains 176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078657 restraints weight = 25966.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081445 restraints weight = 13791.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083340 restraints weight = 9007.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084655 restraints weight = 6716.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085555 restraints weight = 5463.386| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10401 Z= 0.125 Angle : 0.712 12.789 14112 Z= 0.335 Chirality : 0.041 0.266 1607 Planarity : 0.004 0.061 1784 Dihedral : 4.828 75.019 1450 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.10 % Allowed : 21.45 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1275 helix: 1.23 (0.19), residues: 789 sheet: 0.40 (0.47), residues: 126 loop : -1.18 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 38 TYR 0.021 0.001 TYR B 92 PHE 0.035 0.001 PHE B 38 TRP 0.009 0.001 TRP C 36 HIS 0.008 0.001 HIS A 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10399) covalent geometry : angle 0.71186 / 0.33 (14108) SS BOND : bond 0.00147 / 0.07 ( 2) SS BOND : angle 1.04485 / 0.50 ( 4) hydrogen bonds : bond 0.03643 / 2.43 ( 575) hydrogen bonds : angle 3.98429 / 2.84 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1765.66 seconds wall clock time: 31 minutes 12.31 seconds (1872.31 seconds total)