Starting phenix.real_space_refine on Wed Feb 4 06:14:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n61_49045/02_2026/9n61_49045.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n61_49045/02_2026/9n61_49045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n61_49045/02_2026/9n61_49045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n61_49045/02_2026/9n61_49045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n61_49045/02_2026/9n61_49045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n61_49045/02_2026/9n61_49045.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 5618 2.51 5 N 1533 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8862 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4405 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 21, 'TRANS': 548} Chain: "B" Number of atoms: 4312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4312 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 20, 'TRANS': 530} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 83 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 8862 At special positions: 0 Unit cell: (75.864, 102.024, 147.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 1665 8.00 N 1533 7.00 C 5618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 340.6 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 68.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.623A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 removed outlier: 3.623A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.898A pdb=" N LEU A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 270 removed outlier: 3.830A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.604A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 279' Processing helix chain 'A' and resid 280 through 324 removed outlier: 3.575A pdb=" N VAL A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 319 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.533A pdb=" N VAL A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 382 through 435 removed outlier: 3.526A pdb=" N ILE A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 428 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 474 removed outlier: 3.746A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.652A pdb=" N GLN A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 580 removed outlier: 3.559A pdb=" N HIS A 578 " --> pdb=" O HIS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.710A pdb=" N ALA A 600 " --> pdb=" O GLN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 620 removed outlier: 4.223A pdb=" N ILE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 613 " --> pdb=" O MET A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.585A pdb=" N ASP A 633 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.792A pdb=" N GLY A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 641 " --> pdb=" O GLU A 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 637 through 641' Processing helix chain 'A' and resid 644 through 656 removed outlier: 3.534A pdb=" N ARG A 655 " --> pdb=" O VAL A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 687 removed outlier: 3.730A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 removed outlier: 3.651A pdb=" N SER A 693 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 removed outlier: 3.851A pdb=" N VAL A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.931A pdb=" N MET A 730 " --> pdb=" O HIS A 726 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 731 " --> pdb=" O GLN A 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 731' Processing helix chain 'A' and resid 735 through 742 removed outlier: 4.320A pdb=" N MET A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 740 " --> pdb=" O TYR A 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 removed outlier: 3.752A pdb=" N SER B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 removed outlier: 3.754A pdb=" N LEU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.505A pdb=" N ARG B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 234 removed outlier: 5.004A pdb=" N SER B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 4.022A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.782A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 266 through 289 Processing helix chain 'B' and resid 291 through 338 removed outlier: 4.198A pdb=" N LEU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.504A pdb=" N ALA B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 334 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.579A pdb=" N PHE B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 400 removed outlier: 3.570A pdb=" N CYS B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 439 removed outlier: 3.739A pdb=" N TYR B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.615A pdb=" N PHE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 448 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.528A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.977A pdb=" N TYR B 537 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 544 removed outlier: 3.601A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.774A pdb=" N VAL B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 removed outlier: 3.503A pdb=" N GLN B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 614 " --> pdb=" O GLY B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 removed outlier: 3.897A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.612A pdb=" N THR B 665 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.514A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.718A pdb=" N ALA A 582 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASP A 667 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL A 584 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 699 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 666 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 533 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU A 713 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA A 535 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU A 715 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 537 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 716 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 719 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 489 through 493 removed outlier: 4.988A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 468 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.648A pdb=" N THR B 499 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA B 660 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU B 501 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1500 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: 1.41 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2134 1.33 - 1.45: 1728 1.45 - 1.57: 5088 1.57 - 1.69: 10 1.69 - 1.81: 66 Bond restraints: 9026 Sorted by residual: bond pdb=" CA TYR C 3 " pdb=" C TYR C 3 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" CA LYS C 5 " pdb=" C LYS C 5 " ideal model delta sigma weight residual 1.524 1.479 0.044 1.31e-02 5.83e+03 1.14e+01 bond pdb=" N THR B 665 " pdb=" CA THR B 665 " ideal model delta sigma weight residual 1.455 1.413 0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" CA GLN C 4 " pdb=" C GLN C 4 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.17e-02 7.31e+03 8.94e+00 bond pdb=" CA VAL B 666 " pdb=" C VAL B 666 " ideal model delta sigma weight residual 1.523 1.489 0.034 1.27e-02 6.20e+03 6.97e+00 ... (remaining 9021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11928 1.93 - 3.85: 251 3.85 - 5.78: 42 5.78 - 7.70: 25 7.70 - 9.63: 5 Bond angle restraints: 12251 Sorted by residual: angle pdb=" C THR B 665 " pdb=" N VAL B 666 " pdb=" CA VAL B 666 " ideal model delta sigma weight residual 121.97 115.25 6.72 1.80e+00 3.09e-01 1.39e+01 angle pdb=" CA MET B 592 " pdb=" CB MET B 592 " pdb=" CG MET B 592 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CA TYR A 736 " pdb=" CB TYR A 736 " pdb=" CG TYR A 736 " ideal model delta sigma weight residual 113.90 120.48 -6.58 1.80e+00 3.09e-01 1.34e+01 angle pdb=" C ASP B 647 " pdb=" CA ASP B 647 " pdb=" CB ASP B 647 " ideal model delta sigma weight residual 111.50 117.38 -5.88 1.64e+00 3.72e-01 1.29e+01 angle pdb=" C GLN B 676 " pdb=" N GLU B 677 " pdb=" CA GLU B 677 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 ... (remaining 12246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4574 17.57 - 35.14: 636 35.14 - 52.71: 185 52.71 - 70.28: 39 70.28 - 87.85: 20 Dihedral angle restraints: 5454 sinusoidal: 2207 harmonic: 3247 Sorted by residual: dihedral pdb=" C ASP B 647 " pdb=" N ASP B 647 " pdb=" CA ASP B 647 " pdb=" CB ASP B 647 " ideal model delta harmonic sigma weight residual -122.60 -132.04 9.44 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" CA PHE A 275 " pdb=" C PHE A 275 " pdb=" N PHE A 276 " pdb=" CA PHE A 276 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN B 436 " pdb=" CB ASN B 436 " pdb=" CG ASN B 436 " pdb=" OD1 ASN B 436 " ideal model delta sinusoidal sigma weight residual -90.00 -164.31 74.31 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1128 0.050 - 0.101: 234 0.101 - 0.151: 50 0.151 - 0.202: 1 0.202 - 0.252: 3 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA ASP B 647 " pdb=" N ASP B 647 " pdb=" C ASP B 647 " pdb=" CB ASP B 647 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE A 248 " pdb=" N ILE A 248 " pdb=" C ILE A 248 " pdb=" CB ILE A 248 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU B 637 " pdb=" CB LEU B 637 " pdb=" CD1 LEU B 637 " pdb=" CD2 LEU B 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1413 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 664 " -0.023 2.00e-02 2.50e+03 4.83e-02 2.34e+01 pdb=" C GLN B 664 " 0.084 2.00e-02 2.50e+03 pdb=" O GLN B 664 " -0.032 2.00e-02 2.50e+03 pdb=" N THR B 665 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 185 " 0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO B 186 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 186 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 186 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 647 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CG ASP B 647 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASP B 647 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP B 647 " -0.021 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2657 2.82 - 3.34: 8058 3.34 - 3.86: 13975 3.86 - 4.38: 15608 4.38 - 4.90: 26689 Nonbonded interactions: 66987 Sorted by model distance: nonbonded pdb=" OE1 GLN A 277 " pdb=" OH TYR A 555 " model vdw 2.295 3.040 nonbonded pdb=" O HIS A 622 " pdb=" OG SER A 626 " model vdw 2.297 3.040 nonbonded pdb=" O MET A 285 " pdb=" OG1 THR A 289 " model vdw 2.300 3.040 nonbonded pdb=" O GLU A 290 " pdb=" OG1 THR A 294 " model vdw 2.318 3.040 nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.326 3.040 ... (remaining 66982 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9026 Z= 0.207 Angle : 0.740 9.625 12251 Z= 0.392 Chirality : 0.044 0.252 1416 Planarity : 0.005 0.086 1565 Dihedral : 18.307 87.854 3370 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.21 % Allowed : 23.62 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.21), residues: 1124 helix: -2.77 (0.13), residues: 697 sheet: 2.21 (0.71), residues: 60 loop : -0.74 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 333 TYR 0.015 0.001 TYR C 3 PHE 0.043 0.002 PHE B 157 TRP 0.012 0.001 TRP B 648 HIS 0.014 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9026) covalent geometry : angle 0.74050 (12251) hydrogen bonds : bond 0.31896 ( 508) hydrogen bonds : angle 8.78523 ( 1500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 666 LEU cc_start: 0.9106 (mt) cc_final: 0.8892 (mp) REVERT: A 684 LEU cc_start: 0.9311 (tp) cc_final: 0.9066 (pp) REVERT: B 390 LEU cc_start: 0.8490 (tp) cc_final: 0.8239 (tt) outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.1029 time to fit residues: 13.6097 Evaluate side-chains 55 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A 586 GLN A 741 GLN B 384 HIS B 594 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.047636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.035274 restraints weight = 50126.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036477 restraints weight = 24791.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037321 restraints weight = 15810.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.037878 restraints weight = 11746.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.038172 restraints weight = 9599.547| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9026 Z= 0.145 Angle : 0.616 10.461 12251 Z= 0.318 Chirality : 0.039 0.131 1416 Planarity : 0.004 0.051 1565 Dihedral : 8.636 89.149 1299 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.29 % Allowed : 23.31 % Favored : 74.40 % 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: 0.32 (0.25), residues: 1124 helix: 0.53 (0.19), residues: 703 sheet: 2.24 (0.71), residues: 64 loop : -0.64 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 327 TYR 0.020 0.001 TYR C 3 PHE 0.017 0.001 PHE A 505 TRP 0.009 0.001 TRP A 348 HIS 0.008 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9026) covalent geometry : angle 0.61644 (12251) hydrogen bonds : bond 0.07217 ( 508) hydrogen bonds : angle 4.25940 ( 1500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8804 (mp) REVERT: A 357 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8362 (mtm-85) REVERT: A 420 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8624 (ppp) REVERT: A 666 LEU cc_start: 0.9662 (mt) cc_final: 0.9433 (mp) REVERT: A 684 LEU cc_start: 0.9565 (tp) cc_final: 0.9360 (pp) REVERT: C 5 LYS cc_start: 0.8518 (pptt) cc_final: 0.8267 (pptt) outliers start: 22 outliers final: 9 residues processed: 78 average time/residue: 0.0980 time to fit residues: 10.9397 Evaluate side-chains 67 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 9 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.047443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035252 restraints weight = 49843.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.036445 restraints weight = 24728.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.037283 restraints weight = 15720.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037825 restraints weight = 11631.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.038214 restraints weight = 9525.106| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9026 Z= 0.126 Angle : 0.528 9.378 12251 Z= 0.269 Chirality : 0.038 0.121 1416 Planarity : 0.003 0.038 1565 Dihedral : 8.295 85.418 1296 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.25 % Allowed : 24.66 % Favored : 74.09 % 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: 1.57 (0.26), residues: 1124 helix: 1.65 (0.20), residues: 719 sheet: 1.67 (0.68), residues: 76 loop : -0.40 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 210 TYR 0.008 0.001 TYR B 376 PHE 0.012 0.001 PHE A 505 TRP 0.007 0.001 TRP A 308 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9026) covalent geometry : angle 0.52824 (12251) hydrogen bonds : bond 0.05662 ( 508) hydrogen bonds : angle 3.82489 ( 1500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 666 LEU cc_start: 0.9665 (mt) cc_final: 0.9434 (mp) REVERT: B 300 MET cc_start: 0.8860 (tpp) cc_final: 0.8600 (mmm) REVERT: C 5 LYS cc_start: 0.8445 (pptt) cc_final: 0.8174 (pptt) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 0.1036 time to fit residues: 10.4872 Evaluate side-chains 57 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 547 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.034789 restraints weight = 51101.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.035989 restraints weight = 25112.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.036813 restraints weight = 15869.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.037346 restraints weight = 11728.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.037715 restraints weight = 9612.313| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9026 Z= 0.140 Angle : 0.554 11.797 12251 Z= 0.276 Chirality : 0.038 0.134 1416 Planarity : 0.003 0.035 1565 Dihedral : 8.022 85.055 1296 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.77 % Allowed : 25.29 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.26), residues: 1124 helix: 2.11 (0.20), residues: 720 sheet: 1.64 (0.68), residues: 76 loop : -0.27 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.008 0.001 TYR B 376 PHE 0.010 0.001 PHE A 479 TRP 0.006 0.001 TRP B 263 HIS 0.002 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9026) covalent geometry : angle 0.55444 (12251) hydrogen bonds : bond 0.05045 ( 508) hydrogen bonds : angle 3.75117 ( 1500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 202 MET cc_start: 0.8901 (ptp) cc_final: 0.8692 (ptp) REVERT: A 246 ASP cc_start: 0.9274 (m-30) cc_final: 0.8983 (m-30) REVERT: A 357 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8380 (mtm-85) REVERT: A 653 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9491 (mm) REVERT: B 300 MET cc_start: 0.8919 (tpp) cc_final: 0.8582 (mmm) REVERT: B 389 MET cc_start: 0.7912 (tmm) cc_final: 0.7690 (tmm) REVERT: C 5 LYS cc_start: 0.8487 (pptt) cc_final: 0.8162 (pptt) REVERT: C 6 SER cc_start: 0.8962 (p) cc_final: 0.8363 (p) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.0850 time to fit residues: 8.8470 Evaluate side-chains 70 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 547 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.0570 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.0170 chunk 96 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.035695 restraints weight = 49988.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.036941 restraints weight = 24525.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.037784 restraints weight = 15424.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.038354 restraints weight = 11345.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038716 restraints weight = 9227.292| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9026 Z= 0.102 Angle : 0.514 9.126 12251 Z= 0.255 Chirality : 0.038 0.149 1416 Planarity : 0.003 0.036 1565 Dihedral : 7.860 83.745 1296 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.66 % Allowed : 26.33 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.26), residues: 1124 helix: 2.37 (0.20), residues: 720 sheet: 1.75 (0.68), residues: 76 loop : -0.25 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 484 TYR 0.006 0.001 TYR A 309 PHE 0.009 0.001 PHE A 479 TRP 0.007 0.001 TRP A 308 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 9026) covalent geometry : angle 0.51440 (12251) hydrogen bonds : bond 0.04672 ( 508) hydrogen bonds : angle 3.50972 ( 1500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 246 ASP cc_start: 0.9248 (m-30) cc_final: 0.8965 (m-30) REVERT: A 357 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8247 (mtm-85) REVERT: B 300 MET cc_start: 0.8942 (tpp) cc_final: 0.8683 (mmm) REVERT: B 389 MET cc_start: 0.8077 (tmm) cc_final: 0.7815 (tmm) REVERT: C 6 SER cc_start: 0.9011 (p) cc_final: 0.8362 (p) outliers start: 16 outliers final: 12 residues processed: 73 average time/residue: 0.0702 time to fit residues: 7.3227 Evaluate side-chains 66 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 666 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.047190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.035004 restraints weight = 50379.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.036221 restraints weight = 24879.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037059 restraints weight = 15774.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037621 restraints weight = 11637.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.037971 restraints weight = 9497.906| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9026 Z= 0.132 Angle : 0.534 9.296 12251 Z= 0.266 Chirality : 0.038 0.117 1416 Planarity : 0.003 0.035 1565 Dihedral : 7.684 87.767 1296 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.77 % Allowed : 26.43 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.26), residues: 1124 helix: 2.47 (0.20), residues: 727 sheet: 1.85 (0.67), residues: 75 loop : -0.25 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 327 TYR 0.008 0.001 TYR B 376 PHE 0.009 0.001 PHE A 339 TRP 0.005 0.001 TRP A 348 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9026) covalent geometry : angle 0.53447 (12251) hydrogen bonds : bond 0.04587 ( 508) hydrogen bonds : angle 3.60431 ( 1500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 246 ASP cc_start: 0.9257 (m-30) cc_final: 0.8976 (m-30) REVERT: A 357 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8290 (mtm-85) REVERT: B 285 MET cc_start: 0.8828 (mmm) cc_final: 0.7967 (mpp) REVERT: B 300 MET cc_start: 0.8793 (tpp) cc_final: 0.8514 (mmm) REVERT: B 389 MET cc_start: 0.8004 (tmm) cc_final: 0.7755 (tmm) REVERT: B 394 CYS cc_start: 0.9328 (t) cc_final: 0.8879 (t) outliers start: 17 outliers final: 12 residues processed: 72 average time/residue: 0.0770 time to fit residues: 7.8564 Evaluate side-chains 65 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 666 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.047201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.035037 restraints weight = 50620.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.036255 restraints weight = 24921.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.037083 restraints weight = 15749.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.037654 restraints weight = 11612.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.038015 restraints weight = 9460.771| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9026 Z= 0.124 Angle : 0.546 10.100 12251 Z= 0.270 Chirality : 0.038 0.118 1416 Planarity : 0.003 0.036 1565 Dihedral : 7.586 89.127 1296 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.98 % Allowed : 26.43 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.27), residues: 1124 helix: 2.53 (0.20), residues: 729 sheet: 1.98 (0.68), residues: 75 loop : -0.18 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 327 TYR 0.007 0.001 TYR A 309 PHE 0.009 0.001 PHE A 265 TRP 0.005 0.001 TRP A 308 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9026) covalent geometry : angle 0.54632 (12251) hydrogen bonds : bond 0.04532 ( 508) hydrogen bonds : angle 3.57490 ( 1500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 246 ASP cc_start: 0.9253 (m-30) cc_final: 0.8974 (m-30) REVERT: A 357 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8326 (mtm-85) REVERT: A 609 MET cc_start: 0.9255 (tpt) cc_final: 0.8648 (tpt) REVERT: B 285 MET cc_start: 0.8881 (mmm) cc_final: 0.8096 (mpp) REVERT: B 300 MET cc_start: 0.8776 (tpp) cc_final: 0.8508 (mmm) REVERT: B 389 MET cc_start: 0.7958 (tmm) cc_final: 0.7687 (tmm) REVERT: B 394 CYS cc_start: 0.9281 (t) cc_final: 0.8833 (t) REVERT: B 509 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9007 (ptpp) REVERT: C 8 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7432 (tm-30) outliers start: 19 outliers final: 13 residues processed: 73 average time/residue: 0.0896 time to fit residues: 9.2944 Evaluate side-chains 69 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 8 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.047217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.035109 restraints weight = 50079.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.036322 restraints weight = 24623.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.037149 restraints weight = 15580.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037703 restraints weight = 11490.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.038031 restraints weight = 9371.706| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9026 Z= 0.117 Angle : 0.539 14.248 12251 Z= 0.264 Chirality : 0.038 0.123 1416 Planarity : 0.003 0.036 1565 Dihedral : 7.487 89.970 1296 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.19 % Allowed : 26.33 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.27), residues: 1124 helix: 2.61 (0.20), residues: 729 sheet: 2.05 (0.68), residues: 75 loop : -0.17 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 327 TYR 0.007 0.001 TYR A 309 PHE 0.009 0.001 PHE A 265 TRP 0.005 0.001 TRP A 308 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9026) covalent geometry : angle 0.53889 (12251) hydrogen bonds : bond 0.04444 ( 508) hydrogen bonds : angle 3.55298 ( 1500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 246 ASP cc_start: 0.9249 (m-30) cc_final: 0.8970 (m-30) REVERT: A 357 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8324 (mtm-85) REVERT: A 609 MET cc_start: 0.9250 (tpt) cc_final: 0.8625 (tpt) REVERT: A 684 LEU cc_start: 0.9523 (pt) cc_final: 0.9231 (tp) REVERT: B 285 MET cc_start: 0.8883 (mmm) cc_final: 0.8074 (mpp) REVERT: B 300 MET cc_start: 0.8814 (tpp) cc_final: 0.8573 (mmm) REVERT: B 389 MET cc_start: 0.7998 (tmm) cc_final: 0.7739 (tmm) REVERT: B 394 CYS cc_start: 0.9246 (t) cc_final: 0.8798 (t) REVERT: B 509 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8994 (ptpp) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.0838 time to fit residues: 8.7980 Evaluate side-chains 71 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 666 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.047259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.035161 restraints weight = 50268.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.036371 restraints weight = 24702.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037197 restraints weight = 15619.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037738 restraints weight = 11499.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038097 restraints weight = 9423.830| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9026 Z= 0.118 Angle : 0.553 13.311 12251 Z= 0.268 Chirality : 0.038 0.119 1416 Planarity : 0.003 0.036 1565 Dihedral : 7.395 88.894 1296 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.87 % Allowed : 26.64 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.26), residues: 1124 helix: 2.66 (0.20), residues: 728 sheet: 2.73 (0.70), residues: 63 loop : -0.25 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 327 TYR 0.007 0.001 TYR A 309 PHE 0.009 0.001 PHE A 265 TRP 0.005 0.001 TRP A 308 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9026) covalent geometry : angle 0.55335 (12251) hydrogen bonds : bond 0.04387 ( 508) hydrogen bonds : angle 3.54716 ( 1500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 246 ASP cc_start: 0.9248 (m-30) cc_final: 0.8969 (m-30) REVERT: A 357 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8389 (mtm-85) REVERT: A 459 GLU cc_start: 0.9228 (tm-30) cc_final: 0.9007 (pp20) REVERT: A 609 MET cc_start: 0.9245 (tpt) cc_final: 0.8626 (tpt) REVERT: A 684 LEU cc_start: 0.9543 (pt) cc_final: 0.9239 (tp) REVERT: B 260 MET cc_start: 0.8919 (mtm) cc_final: 0.8698 (mtm) REVERT: B 300 MET cc_start: 0.8831 (tpp) cc_final: 0.8622 (mmm) REVERT: B 389 MET cc_start: 0.8018 (tmm) cc_final: 0.7793 (tmm) REVERT: B 394 CYS cc_start: 0.9220 (t) cc_final: 0.8770 (t) REVERT: B 509 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8979 (ptpp) REVERT: C 8 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7459 (tm-30) outliers start: 18 outliers final: 15 residues processed: 72 average time/residue: 0.0907 time to fit residues: 9.0900 Evaluate side-chains 72 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 8 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.035417 restraints weight = 50446.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.036627 restraints weight = 24441.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037453 restraints weight = 15389.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038010 restraints weight = 11316.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.038367 restraints weight = 9198.937| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9026 Z= 0.113 Angle : 0.548 13.102 12251 Z= 0.267 Chirality : 0.038 0.124 1416 Planarity : 0.002 0.036 1565 Dihedral : 7.303 87.965 1296 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.87 % Allowed : 26.53 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.27), residues: 1124 helix: 2.68 (0.20), residues: 729 sheet: 2.79 (0.70), residues: 63 loop : -0.23 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 327 TYR 0.007 0.001 TYR A 309 PHE 0.009 0.001 PHE A 265 TRP 0.005 0.001 TRP A 308 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9026) covalent geometry : angle 0.54822 (12251) hydrogen bonds : bond 0.04297 ( 508) hydrogen bonds : angle 3.51358 ( 1500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 246 ASP cc_start: 0.9251 (m-30) cc_final: 0.8977 (m-30) REVERT: A 357 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8386 (mtm-85) REVERT: A 684 LEU cc_start: 0.9552 (pt) cc_final: 0.9253 (tp) REVERT: B 260 MET cc_start: 0.8904 (mtm) cc_final: 0.8685 (mtm) REVERT: B 285 MET cc_start: 0.8846 (mmm) cc_final: 0.7583 (mpp) REVERT: B 300 MET cc_start: 0.8795 (tpp) cc_final: 0.8503 (mmm) REVERT: B 389 MET cc_start: 0.8023 (tmm) cc_final: 0.7801 (tmm) REVERT: B 394 CYS cc_start: 0.9188 (t) cc_final: 0.8744 (t) REVERT: B 509 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8958 (ptpp) REVERT: C 8 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7453 (tm-30) outliers start: 18 outliers final: 15 residues processed: 72 average time/residue: 0.0853 time to fit residues: 8.4546 Evaluate side-chains 72 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 8 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 103 optimal weight: 0.0470 chunk 10 optimal weight: 0.0270 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.048121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035846 restraints weight = 49781.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.037092 restraints weight = 24426.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037924 restraints weight = 15525.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.038478 restraints weight = 11503.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.038854 restraints weight = 9422.688| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9026 Z= 0.102 Angle : 0.549 13.130 12251 Z= 0.263 Chirality : 0.038 0.129 1416 Planarity : 0.002 0.036 1565 Dihedral : 7.220 88.211 1296 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.66 % Allowed : 26.74 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.27), residues: 1124 helix: 2.80 (0.20), residues: 721 sheet: 2.87 (0.71), residues: 63 loop : -0.22 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 333 TYR 0.007 0.001 TYR C 3 PHE 0.009 0.001 PHE A 265 TRP 0.006 0.001 TRP A 308 HIS 0.002 0.000 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9026) covalent geometry : angle 0.54941 (12251) hydrogen bonds : bond 0.04097 ( 508) hydrogen bonds : angle 3.42846 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.38 seconds wall clock time: 22 minutes 32.94 seconds (1352.94 seconds total)