Starting phenix.real_space_refine on Sat Jul 4 06:53:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e5z_30995/07_2026/7e5z_30995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e5z_30995/07_2026/7e5z_30995.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e5z_30995/07_2026/7e5z_30995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e5z_30995/07_2026/7e5z_30995.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7e5z_30995/07_2026/7e5z_30995.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e5z_30995/07_2026/7e5z_30995.cif" model { file = "/net/cci-nas-00/data/ceres_data/7e5z_30995/07_2026/7e5z_30995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e5z_30995/07_2026/7e5z_30995.cif" } 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= 0.007 sd= 0.034 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: 8 Type Number sf(0) Gaussians W 1 12.54 5 Fe 20 7.16 5 P 5 5.49 5 S 85 5.16 5 C 6389 2.51 5 N 1820 2.21 5 O 1924 1.98 5 H 8810 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19054 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 11141 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 45, 'TRANS': 729} Chain breaks: 1 Chain: "B" Number of atoms: 7747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 7747 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 27, 'TRANS': 509} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {' W': 1, 'FES': 1, 'MGD': 2, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 490 SG CYS A 102 52.690 29.667 81.735 1.00 78.33 S ATOM 676 SG CYS A 115 53.012 27.443 83.224 1.00 81.48 S ATOM 717 SG CYS A 118 57.786 28.789 83.440 1.00 82.89 S ATOM 884 SG CYS A 132 57.079 32.544 81.745 1.00 84.97 S ATOM 2092 SG CYS A 216 45.893 27.696 77.991 1.00 82.89 S ATOM 2057 SG CYS A 213 40.458 26.953 80.445 1.00 83.96 S ATOM 2740 SG CYS A 266 42.889 24.929 74.851 1.00 80.21 S ATOM 2133 SG CYS A 219 42.000 29.786 75.167 1.00 83.24 S ATOM 2191 SG CYS A 223 39.836 35.677 69.737 1.00 81.05 S ATOM 2686 SG CYS A 262 40.099 31.233 69.550 1.00 80.67 S ATOM 2639 SG CYS A 256 35.005 33.064 66.998 1.00 83.00 S ATOM 2657 SG CYS A 259 39.457 35.799 65.522 1.00 78.47 S ATOM 2191 SG CYS A 223 39.836 35.677 69.737 1.00 81.05 S ATOM 2657 SG CYS A 259 39.457 35.799 65.522 1.00 78.47 S ATOM 3176 SG CYS A 295 45.936 34.087 52.188 1.00 86.22 S ATOM 3667 SG CYS A 329 41.258 35.643 56.111 1.00 76.61 S ATOM 3219 SG CYS A 298 41.732 38.713 51.901 1.00 88.24 S ATOM 3176 SG CYS A 295 45.936 34.087 52.188 1.00 86.22 S ATOM 3257 SG CYS A 302 47.040 36.431 55.411 1.00 80.77 S ATOM 18110 SG CYS B 502 45.093 35.317 92.305 1.00 79.77 S ATOM 18610 SG CYS B 542 48.649 35.148 95.664 1.00 83.44 S ATOM 18176 SG CYS B 508 45.577 30.724 93.567 1.00 84.21 S ATOM 18140 SG CYS B 505 48.800 31.120 92.714 1.00 84.95 S ATOM 18610 SG CYS B 542 48.649 35.148 95.664 1.00 83.44 S ATOM 18110 SG CYS B 502 45.093 35.317 92.305 1.00 79.77 S ATOM 18176 SG CYS B 508 45.577 30.724 93.567 1.00 84.21 S ATOM 12410 SG CYS B 113 31.884 36.456 110.142 1.00 78.16 S ATOM 12451 SG CYS B 118 31.038 37.209 113.136 1.00 77.35 S ATOM 12874 SG CYS B 146 35.767 39.161 109.530 1.00 80.98 S ATOM 12924 SG CYS B 150 36.341 38.978 113.213 1.00 78.95 S Time building chain proxies: 3.51, per 1000 atoms: 0.18 Number of scatterers: 19054 At special positions: 0 Unit cell: (88.81, 89.64, 142.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) W 1 73.95 Fe 20 26.01 S 85 16.00 P 5 15.00 O 1924 8.00 N 1820 7.00 C 6389 6.00 H 8810 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 774.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1003 " pdb="FE2 FES A1003 " - pdb=" SG CYS A 132 " pdb="FE2 FES A1003 " - pdb=" SG CYS A 118 " pdb="FE1 FES A1003 " - pdb=" SG CYS A 102 " pdb="FE1 FES A1003 " - pdb=" SG CYS A 115 " pdb=" FES B1002 " pdb="FE2 FES B1002 " - pdb=" SG CYS B 146 " pdb="FE1 FES B1002 " - pdb=" SG CYS B 113 " pdb="FE2 FES B1002 " - pdb=" SG CYS B 150 " pdb="FE1 FES B1002 " - pdb=" SG CYS B 118 " pdb=" SF4 A1004 " pdb="FE3 SF4 A1004 " - pdb=" SG CYS A 266 " pdb="FE1 SF4 A1004 " - pdb=" SG CYS A 216 " pdb="FE2 SF4 A1004 " - pdb=" SG CYS A 213 " pdb="FE4 SF4 A1004 " - pdb=" SG CYS A 219 " pdb=" SF4 A1005 " pdb="FE4 SF4 A1005 " - pdb=" SG CYS A 259 " pdb="FE4 SF4 A1005 " - pdb=" SG CYS A 223 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 256 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 262 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 329 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 302 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 295 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 298 " pdb=" SF4 B1001 " pdb="FE1 SF4 B1001 " - pdb=" SG CYS B 542 " pdb="FE2 SF4 B1001 " - pdb=" SG CYS B 508 " pdb="FE4 SF4 B1001 " - pdb=" SG CYS B 502 " pdb="FE3 SF4 B1001 " - pdb=" SG CYS B 505 " Number of angles added : 62 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 41.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 147 through 163 Processing helix chain 'A' and resid 166 through 170 removed outlier: 4.299A pdb=" N SER A 170 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 378 through 396 removed outlier: 4.058A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 424 removed outlier: 3.634A pdb=" N TYR A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.673A pdb=" N VAL A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 519 through 535 removed outlier: 4.091A pdb=" N MET A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 545 removed outlier: 3.528A pdb=" N ILE A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.847A pdb=" N LEU A 575 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 removed outlier: 3.903A pdb=" N SER A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.911A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 removed outlier: 4.629A pdb=" N LEU A 614 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 640 Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 687 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 711 through 717 removed outlier: 4.270A pdb=" N LEU A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET A 717 " --> pdb=" O HIS A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 785 removed outlier: 3.827A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 779 " --> pdb=" O TRP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 803 removed outlier: 4.637A pdb=" N ALA A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 809 Processing helix chain 'A' and resid 812 through 818 Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.706A pdb=" N GLU B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 68 through 79 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.733A pdb=" N VAL B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 removed outlier: 3.693A pdb=" N PHE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 167 through 177 removed outlier: 4.183A pdb=" N ALA B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 4.042A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 removed outlier: 3.645A pdb=" N GLU B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.533A pdb=" N LEU B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 271 through 287 removed outlier: 4.346A pdb=" N PHE B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 removed outlier: 3.983A pdb=" N ALA B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 369 through 375 removed outlier: 3.510A pdb=" N TRP B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.571A pdb=" N ARG B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 420 through 427 removed outlier: 3.524A pdb=" N LEU B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 4.187A pdb=" N THR B 464 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU B 465 " --> pdb=" O PHE B 462 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLU B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS B 467 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 469 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.776A pdb=" N ALA B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 519 removed outlier: 4.160A pdb=" N GLN B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 539 Processing helix chain 'B' and resid 549 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.923A pdb=" N GLU A 73 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 removed outlier: 3.566A pdb=" N MET A 272 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 294 removed outlier: 3.786A pdb=" N ARG A 289 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 308 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 291 " --> pdb=" O TYR A 306 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A 305 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA A 316 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 307 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AA5, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA6, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.597A pdb=" N GLN A 652 " --> pdb=" O TYR A 648 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 67 removed outlier: 6.665A pdb=" N ILE B 66 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 144 removed outlier: 6.892A pdb=" N ILE B 110 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 144 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL B 112 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 249 through 251 removed outlier: 3.942A pdb=" N LEU B 366 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 251 " --> pdb=" O LEU B 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 399 through 403 removed outlier: 3.552A pdb=" N VAL B 403 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 411 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 451 through 452 313 hydrogen bonds defined for protein. 870 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: 4.27 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 8800 1.13 - 1.42: 4376 1.42 - 1.71: 5978 1.71 - 2.00: 94 2.00 - 2.29: 56 Bond restraints: 19304 Sorted by residual: bond pdb=" C LEU A 612 " pdb=" O LEU A 612 " ideal model delta sigma weight residual 1.236 1.305 -0.068 1.15e-02 7.56e+03 3.52e+01 bond pdb=" N LEU A 612 " pdb=" CA LEU A 612 " ideal model delta sigma weight residual 1.459 1.513 -0.054 1.19e-02 7.06e+03 2.07e+01 bond pdb=" C10 MGD A1002 " pdb=" O3A MGD A1002 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N ILE A 615 " pdb=" CA ILE A 615 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.33e-02 5.65e+03 1.18e+01 bond pdb=" C10 MGD A1001 " pdb=" O3A MGD A1001 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 19299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 34260 4.12 - 8.25: 66 8.25 - 12.37: 20 12.37 - 16.49: 2 16.49 - 20.62: 6 Bond angle restraints: 34354 Sorted by residual: angle pdb=" S1 FES A1003 " pdb="FE2 FES A1003 " pdb=" S2 FES A1003 " ideal model delta sigma weight residual 104.33 86.51 17.82 1.14e+00 7.69e-01 2.44e+02 angle pdb=" S1 FES B1002 " pdb="FE2 FES B1002 " pdb=" S2 FES B1002 " ideal model delta sigma weight residual 104.33 87.36 16.97 1.14e+00 7.69e-01 2.21e+02 angle pdb=" S1 FES A1003 " pdb="FE1 FES A1003 " pdb=" S2 FES A1003 " ideal model delta sigma weight residual 104.33 86.48 17.85 1.20e+00 6.94e-01 2.21e+02 angle pdb=" S1 FES B1002 " pdb="FE1 FES B1002 " pdb=" S2 FES B1002 " ideal model delta sigma weight residual 104.33 87.36 16.97 1.20e+00 6.94e-01 2.00e+02 angle pdb="FE1 FES A1003 " pdb=" S2 FES A1003 " pdb="FE2 FES A1003 " ideal model delta sigma weight residual 75.66 85.97 -10.31 1.14e+00 7.69e-01 8.18e+01 ... (remaining 34349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8912 35.43 - 70.86: 267 70.86 - 106.30: 16 106.30 - 141.73: 0 141.73 - 177.16: 1 Dihedral angle restraints: 9196 sinusoidal: 4943 harmonic: 4253 Sorted by residual: dihedral pdb=" C10 FMN B1000 " pdb=" C1' FMN B1000 " pdb=" N10 FMN B1000 " pdb=" C2' FMN B1000 " ideal model delta sinusoidal sigma weight residual -102.41 74.75 -177.16 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA ARG A 237 " pdb=" C ARG A 237 " pdb=" N ALA A 238 " pdb=" CA ALA A 238 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C ALA B 153 " pdb=" N ALA B 153 " pdb=" CA ALA B 153 " pdb=" CB ALA B 153 " ideal model delta harmonic sigma weight residual -122.60 -134.15 11.55 0 2.50e+00 1.60e-01 2.13e+01 ... (remaining 9193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1412 0.077 - 0.154: 146 0.154 - 0.232: 6 0.232 - 0.309: 3 0.309 - 0.386: 2 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CA ALA B 153 " pdb=" N ALA B 153 " pdb=" C ALA B 153 " pdb=" CB ALA B 153 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C11 MGD A1001 " pdb=" C10 MGD A1001 " pdb=" C12 MGD A1001 " pdb=" O11 MGD A1001 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C23 MGD A1002 " pdb=" C14 MGD A1002 " pdb=" N22 MGD A1002 " pdb=" O11 MGD A1002 " both_signs ideal model delta sigma weight residual False 2.33 2.59 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1566 not shown) Planarity restraints: 3008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 MGD A1002 " -0.078 2.00e-02 2.50e+03 1.70e-01 7.96e+02 pdb=" C17 MGD A1002 " 0.016 2.00e-02 2.50e+03 pdb=" C19 MGD A1002 " 0.025 2.00e-02 2.50e+03 pdb=" C21 MGD A1002 " -0.152 2.00e-02 2.50e+03 pdb=" C23 MGD A1002 " 0.438 2.00e-02 2.50e+03 pdb=" N15 MGD A1002 " -0.173 2.00e-02 2.50e+03 pdb=" N18 MGD A1002 " 0.071 2.00e-02 2.50e+03 pdb=" N19 MGD A1002 " 0.087 2.00e-02 2.50e+03 pdb=" N20 MGD A1002 " -0.079 2.00e-02 2.50e+03 pdb=" N22 MGD A1002 " -0.212 2.00e-02 2.50e+03 pdb=" O17 MGD A1002 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 MGD A1001 " 0.062 2.00e-02 2.50e+03 1.42e-01 5.55e+02 pdb=" C17 MGD A1001 " -0.014 2.00e-02 2.50e+03 pdb=" C19 MGD A1001 " -0.020 2.00e-02 2.50e+03 pdb=" C21 MGD A1001 " 0.121 2.00e-02 2.50e+03 pdb=" C23 MGD A1001 " -0.363 2.00e-02 2.50e+03 pdb=" N15 MGD A1001 " 0.139 2.00e-02 2.50e+03 pdb=" N18 MGD A1001 " -0.059 2.00e-02 2.50e+03 pdb=" N19 MGD A1001 " -0.074 2.00e-02 2.50e+03 pdb=" N20 MGD A1001 " 0.064 2.00e-02 2.50e+03 pdb=" N22 MGD A1001 " 0.191 2.00e-02 2.50e+03 pdb=" O17 MGD A1001 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 529 " 0.071 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CG ASN A 529 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 529 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 529 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 529 " -0.109 2.00e-02 2.50e+03 pdb="HD22 ASN A 529 " 0.111 2.00e-02 2.50e+03 ... (remaining 3005 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 289 2.05 - 2.69: 28461 2.69 - 3.33: 51198 3.33 - 3.96: 63230 3.96 - 4.60: 99934 Nonbonded interactions: 243112 Sorted by model distance: nonbonded pdb="HD13 LEU A 536 " pdb="HH22 ARG A 584 " model vdw 1.419 2.270 nonbonded pdb=" OG1 THR A 454 " pdb=" H LEU A 626 " model vdw 1.579 2.450 nonbonded pdb=" HB3 PHE A 457 " pdb=" HE1 HIS A 627 " model vdw 1.599 2.270 nonbonded pdb=" H GLN A 82 " pdb=" OE1 GLU A 85 " model vdw 1.621 2.450 nonbonded pdb=" O GLN A 503 " pdb=" HG SER A 506 " model vdw 1.622 2.450 ... (remaining 243107 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.450 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.012 0.895 10519 Z= 0.932 Angle : 2.616 78.218 14365 Z= 0.585 Chirality : 0.048 0.386 1569 Planarity : 0.007 0.170 1865 Dihedral : 14.256 177.162 3799 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.18 % Favored : 89.74 % Rotamer: Outliers : 0.57 % Allowed : 3.33 % Favored : 96.10 % Cbeta Deviations : 0.08 % 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: -6.25 (0.16), residues: 1306 helix: -3.41 (0.18), residues: 446 sheet: -4.61 (0.35), residues: 95 loop : -4.82 (0.15), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 815 TYR 0.009 0.001 TYR A 582 PHE 0.009 0.001 PHE A 744 TRP 0.015 0.001 TRP B 524 HIS 0.008 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.27 (10494) covalent geometry : angle 0.91143 / 0.54 (14303) hydrogen bonds : bond 0.21262 / 14.37 ( 313) hydrogen bonds : angle 8.57260 / 5.98 ( 870) metal coordination : bond 0.13301 / 4.41 ( 24) metal coordination : angle 37.33690 / 23.53 ( 62) Misc. bond : bond 0.89514 / 47.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8120 (tpp) cc_final: 0.7902 (tpt) REVERT: A 472 ASN cc_start: 0.7922 (t0) cc_final: 0.7629 (t0) REVERT: A 545 TYR cc_start: 0.7907 (m-80) cc_final: 0.7474 (m-10) REVERT: B 129 THR cc_start: 0.7611 (m) cc_final: 0.7261 (m) REVERT: B 256 GLU cc_start: 0.7253 (pt0) cc_final: 0.6432 (pt0) REVERT: B 264 ASP cc_start: 0.7306 (m-30) cc_final: 0.7098 (m-30) outliers start: 6 outliers final: 4 residues processed: 192 average time/residue: 0.2293 time to fit residues: 61.2160 Evaluate side-chains 126 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain B residue 154 PRO Chi-restraints excluded: chain B residue 366 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 HIS ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS A 540 GLN A 618 GLN A 636 GLN A 669 GLN A 779 GLN A 831 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088039 restraints weight = 50358.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090479 restraints weight = 20219.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.091923 restraints weight = 9860.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092789 restraints weight = 5496.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093311 restraints weight = 3428.170| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10519 Z= 0.135 Angle : 2.061 71.905 14365 Z= 0.354 Chirality : 0.043 0.163 1569 Planarity : 0.004 0.040 1865 Dihedral : 8.017 178.413 1467 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.65 % Favored : 90.28 % Rotamer: Outliers : 0.76 % Allowed : 8.66 % Favored : 90.58 % 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: -4.89 (0.19), residues: 1306 helix: -2.15 (0.22), residues: 478 sheet: -3.96 (0.40), residues: 98 loop : -4.10 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 507 TYR 0.012 0.001 TYR A 791 PHE 0.016 0.001 PHE A 744 TRP 0.012 0.001 TRP B 524 HIS 0.007 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10494) covalent geometry : angle 0.60734 / 0.31 (14303) hydrogen bonds : bond 0.04419 / 2.97 ( 313) hydrogen bonds : angle 6.35801 / 4.42 ( 870) metal coordination : bond 0.01997 / 1.24 ( 24) metal coordination : angle 29.98867 / 18.93 ( 62) Misc. bond : bond 0.00475 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.7710 (t0) cc_final: 0.7495 (t70) REVERT: A 188 GLU cc_start: 0.7761 (pt0) cc_final: 0.7526 (tt0) REVERT: A 594 MET cc_start: 0.6668 (mmp) cc_final: 0.6429 (mmt) REVERT: B 176 GLU cc_start: 0.7717 (tp30) cc_final: 0.7464 (tp30) REVERT: B 256 GLU cc_start: 0.7799 (pt0) cc_final: 0.6977 (pt0) REVERT: B 264 ASP cc_start: 0.7235 (m-30) cc_final: 0.6888 (m-30) REVERT: B 549 SER cc_start: 0.8731 (m) cc_final: 0.8240 (p) outliers start: 8 outliers final: 4 residues processed: 141 average time/residue: 0.1860 time to fit residues: 39.3998 Evaluate side-chains 119 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 682 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 599 HIS A 710 HIS A 724 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.082530 restraints weight = 60810.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085133 restraints weight = 23928.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086680 restraints weight = 11669.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087642 restraints weight = 6638.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088210 restraints weight = 4181.858| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10519 Z= 0.198 Angle : 1.933 78.571 14365 Z= 0.356 Chirality : 0.045 0.187 1569 Planarity : 0.004 0.040 1865 Dihedral : 7.741 173.948 1460 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.18 % Favored : 89.74 % Rotamer: Outliers : 1.90 % Allowed : 10.18 % Favored : 87.92 % 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: -4.22 (0.20), residues: 1306 helix: -1.57 (0.23), residues: 478 sheet: -3.39 (0.45), residues: 105 loop : -3.76 (0.19), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.011 0.001 TYR A 315 PHE 0.020 0.001 PHE A 744 TRP 0.022 0.001 TRP B 524 HIS 0.008 0.001 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (10494) covalent geometry : angle 0.61512 / 0.32 (14303) hydrogen bonds : bond 0.04846 / 3.23 ( 313) hydrogen bonds : angle 5.99497 / 4.18 ( 870) metal coordination : bond 0.02094 / 1.23 ( 24) metal coordination : angle 27.90773 / 17.58 ( 62) Misc. bond : bond 0.00280 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7422 (mtp180) REVERT: A 112 ASP cc_start: 0.7947 (t0) cc_final: 0.7735 (t70) REVERT: A 119 MET cc_start: 0.8125 (mmm) cc_final: 0.7844 (mmm) REVERT: A 251 MET cc_start: 0.8372 (tmm) cc_final: 0.8107 (tmm) REVERT: A 594 MET cc_start: 0.6833 (mmp) cc_final: 0.6536 (mmt) REVERT: B 256 GLU cc_start: 0.7950 (pt0) cc_final: 0.7284 (pt0) REVERT: B 264 ASP cc_start: 0.7191 (m-30) cc_final: 0.6928 (m-30) REVERT: B 351 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8592 (tppt) outliers start: 20 outliers final: 13 residues processed: 134 average time/residue: 0.2068 time to fit residues: 40.2139 Evaluate side-chains 124 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 105 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.091475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082612 restraints weight = 60153.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085173 restraints weight = 23692.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086685 restraints weight = 11541.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.087610 restraints weight = 6567.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088206 restraints weight = 4166.767| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10519 Z= 0.160 Angle : 1.803 79.610 14365 Z= 0.328 Chirality : 0.043 0.137 1569 Planarity : 0.004 0.043 1865 Dihedral : 7.568 175.514 1460 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.26 % Favored : 90.66 % Rotamer: Outliers : 1.62 % Allowed : 11.70 % Favored : 86.68 % 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: -3.70 (0.22), residues: 1306 helix: -1.15 (0.24), residues: 474 sheet: -2.99 (0.51), residues: 94 loop : -3.46 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 47 TYR 0.010 0.001 TYR A 315 PHE 0.016 0.001 PHE A 744 TRP 0.016 0.001 TRP B 524 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (10494) covalent geometry : angle 0.56426 / 0.29 (14303) hydrogen bonds : bond 0.04101 / 2.71 ( 313) hydrogen bonds : angle 5.74814 / 4.02 ( 870) metal coordination : bond 0.02129 / 1.23 ( 24) metal coordination : angle 26.07596 / 16.47 ( 62) Misc. bond : bond 0.00142 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7502 (mtp180) REVERT: A 594 MET cc_start: 0.6783 (mmp) cc_final: 0.6465 (mmt) REVERT: A 624 THR cc_start: 0.9064 (p) cc_final: 0.8805 (p) REVERT: B 264 ASP cc_start: 0.7315 (m-30) cc_final: 0.6982 (m-30) REVERT: B 351 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8526 (tppt) outliers start: 17 outliers final: 12 residues processed: 128 average time/residue: 0.1894 time to fit residues: 36.2341 Evaluate side-chains 120 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.080244 restraints weight = 60779.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.082747 restraints weight = 24175.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.084242 restraints weight = 11938.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085176 restraints weight = 6871.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.085726 restraints weight = 4454.092| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10519 Z= 0.215 Angle : 1.776 75.371 14365 Z= 0.349 Chirality : 0.045 0.148 1569 Planarity : 0.005 0.065 1865 Dihedral : 7.752 174.749 1460 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.95 % Favored : 88.97 % Rotamer: Outliers : 1.90 % Allowed : 13.80 % Favored : 84.30 % 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: -3.62 (0.22), residues: 1306 helix: -1.08 (0.24), residues: 477 sheet: -3.23 (0.47), residues: 104 loop : -3.36 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 584 TYR 0.011 0.001 TYR A 824 PHE 0.018 0.001 PHE A 744 TRP 0.023 0.001 TRP B 524 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (10494) covalent geometry : angle 0.61208 / 0.32 (14303) hydrogen bonds : bond 0.04585 / 3.05 ( 313) hydrogen bonds : angle 5.76106 / 4.05 ( 870) metal coordination : bond 0.02520 / 1.45 ( 24) metal coordination : angle 25.37730 / 16.16 ( 62) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 CYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7734 (p) REVERT: A 251 MET cc_start: 0.8273 (tmm) cc_final: 0.8024 (tmm) REVERT: A 523 MET cc_start: 0.7696 (ptm) cc_final: 0.7453 (ptm) REVERT: A 594 MET cc_start: 0.6901 (mmp) cc_final: 0.6565 (mmt) REVERT: B 264 ASP cc_start: 0.7374 (m-30) cc_final: 0.6998 (m-30) REVERT: B 351 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8473 (mmtp) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.1751 time to fit residues: 32.8542 Evaluate side-chains 116 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082953 restraints weight = 59244.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085518 restraints weight = 23464.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087065 restraints weight = 11517.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088000 restraints weight = 6542.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088596 restraints weight = 4184.126| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10519 Z= 0.108 Angle : 1.613 66.863 14365 Z= 0.302 Chirality : 0.041 0.134 1569 Planarity : 0.004 0.049 1865 Dihedral : 7.280 179.959 1460 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.50 % Favored : 91.42 % Rotamer: Outliers : 1.62 % Allowed : 15.32 % Favored : 83.06 % 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: -3.04 (0.23), residues: 1306 helix: -0.62 (0.25), residues: 472 sheet: -2.63 (0.54), residues: 92 loop : -3.04 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 584 TYR 0.010 0.001 TYR A 315 PHE 0.016 0.001 PHE A 744 TRP 0.013 0.001 TRP A 197 HIS 0.002 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10494) covalent geometry : angle 0.52863 / 0.27 (14303) hydrogen bonds : bond 0.03558 / 2.37 ( 313) hydrogen bonds : angle 5.37644 / 3.78 ( 870) metal coordination : bond 0.01408 / 0.83 ( 24) metal coordination : angle 23.20771 / 14.79 ( 62) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 CYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7603 (p) REVERT: A 251 MET cc_start: 0.8183 (tmm) cc_final: 0.7903 (tmm) REVERT: A 523 MET cc_start: 0.7677 (ptm) cc_final: 0.7417 (ptm) REVERT: A 560 THR cc_start: 0.8338 (t) cc_final: 0.8124 (m) REVERT: A 594 MET cc_start: 0.6750 (mmp) cc_final: 0.6533 (mmt) REVERT: B 264 ASP cc_start: 0.7387 (m-30) cc_final: 0.7008 (m-30) REVERT: B 351 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8466 (mmtp) REVERT: B 368 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8266 (m110) outliers start: 17 outliers final: 10 residues processed: 120 average time/residue: 0.1907 time to fit residues: 34.1261 Evaluate side-chains 114 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN A 490 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080032 restraints weight = 63618.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.082570 restraints weight = 25325.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084080 restraints weight = 12557.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085060 restraints weight = 7337.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085676 restraints weight = 4701.524| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10519 Z= 0.198 Angle : 1.706 65.301 14365 Z= 0.336 Chirality : 0.044 0.143 1569 Planarity : 0.004 0.051 1865 Dihedral : 7.471 176.032 1460 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.80 % Favored : 89.13 % Rotamer: Outliers : 1.90 % Allowed : 15.70 % Favored : 82.40 % 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: -3.08 (0.22), residues: 1306 helix: -0.59 (0.25), residues: 474 sheet: -2.94 (0.49), residues: 102 loop : -3.06 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.013 0.001 TYR A 824 PHE 0.016 0.001 PHE A 744 TRP 0.021 0.001 TRP B 524 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (10494) covalent geometry : angle 0.59041 / 0.31 (14303) hydrogen bonds : bond 0.04291 / 2.86 ( 313) hydrogen bonds : angle 5.49680 / 3.86 ( 870) metal coordination : bond 0.02126 / 1.22 ( 24) metal coordination : angle 24.36255 / 15.57 ( 62) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 CYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7726 (p) REVERT: A 251 MET cc_start: 0.8277 (tmm) cc_final: 0.7972 (tmm) REVERT: A 594 MET cc_start: 0.6907 (mmp) cc_final: 0.6644 (mmt) REVERT: B 264 ASP cc_start: 0.7437 (m-30) cc_final: 0.7128 (m-30) REVERT: B 368 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8325 (m110) outliers start: 20 outliers final: 16 residues processed: 119 average time/residue: 0.1628 time to fit residues: 29.4093 Evaluate side-chains 119 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.080116 restraints weight = 63079.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082637 restraints weight = 25080.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084185 restraints weight = 12412.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.085142 restraints weight = 7203.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085668 restraints weight = 4604.423| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10519 Z= 0.178 Angle : 1.684 63.807 14365 Z= 0.327 Chirality : 0.043 0.137 1569 Planarity : 0.004 0.048 1865 Dihedral : 7.476 177.489 1460 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.57 % Favored : 89.36 % Rotamer: Outliers : 2.09 % Allowed : 16.37 % Favored : 81.54 % 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: -3.01 (0.22), residues: 1306 helix: -0.54 (0.25), residues: 473 sheet: -3.00 (0.50), residues: 89 loop : -3.00 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.012 0.001 TYR A 824 PHE 0.016 0.001 PHE A 744 TRP 0.020 0.001 TRP B 524 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10494) covalent geometry : angle 0.57394 / 0.30 (14303) hydrogen bonds : bond 0.04092 / 2.72 ( 313) hydrogen bonds : angle 5.44594 / 3.82 ( 870) metal coordination : bond 0.02019 / 1.17 ( 24) metal coordination : angle 24.09794 / 15.50 ( 62) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 CYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7700 (p) REVERT: A 251 MET cc_start: 0.8275 (tmm) cc_final: 0.7972 (tmm) REVERT: A 560 THR cc_start: 0.8369 (t) cc_final: 0.8097 (m) REVERT: A 594 MET cc_start: 0.6866 (mmp) cc_final: 0.6583 (mmt) REVERT: B 168 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7090 (tt) REVERT: B 264 ASP cc_start: 0.7449 (m-30) cc_final: 0.7146 (m-30) outliers start: 22 outliers final: 16 residues processed: 118 average time/residue: 0.1532 time to fit residues: 27.9359 Evaluate side-chains 120 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.090300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.081273 restraints weight = 62652.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.083818 restraints weight = 24573.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085356 restraints weight = 12075.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086326 restraints weight = 6967.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086862 restraints weight = 4414.511| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10519 Z= 0.130 Angle : 1.634 62.594 14365 Z= 0.308 Chirality : 0.042 0.134 1569 Planarity : 0.004 0.050 1865 Dihedral : 7.208 178.139 1460 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.03 % Favored : 89.89 % Rotamer: Outliers : 1.62 % Allowed : 16.65 % Favored : 81.73 % 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: -2.75 (0.23), residues: 1306 helix: -0.35 (0.25), residues: 474 sheet: -2.64 (0.48), residues: 97 loop : -2.86 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 580 TYR 0.011 0.001 TYR A 824 PHE 0.015 0.001 PHE A 744 TRP 0.013 0.001 TRP B 524 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10494) covalent geometry : angle 0.54034 / 0.28 (14303) hydrogen bonds : bond 0.03631 / 2.42 ( 313) hydrogen bonds : angle 5.24949 / 3.68 ( 870) metal coordination : bond 0.01518 / 0.89 ( 24) metal coordination : angle 23.48261 / 15.05 ( 62) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7674 (p) REVERT: A 135 THR cc_start: 0.9316 (t) cc_final: 0.8892 (m) REVERT: A 251 MET cc_start: 0.8197 (tmm) cc_final: 0.7931 (tmm) REVERT: A 560 THR cc_start: 0.8319 (t) cc_final: 0.8108 (m) REVERT: A 594 MET cc_start: 0.6813 (mmp) cc_final: 0.6548 (mmt) outliers start: 17 outliers final: 14 residues processed: 120 average time/residue: 0.1739 time to fit residues: 31.3740 Evaluate side-chains 119 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 501 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 70 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078344 restraints weight = 64820.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.080850 restraints weight = 25742.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082344 restraints weight = 12746.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.083304 restraints weight = 7497.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.083902 restraints weight = 4850.092| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10519 Z= 0.259 Angle : 1.772 67.436 14365 Z= 0.369 Chirality : 0.047 0.155 1569 Planarity : 0.005 0.048 1865 Dihedral : 7.669 175.804 1460 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.72 % Favored : 88.21 % Rotamer: Outliers : 2.00 % Allowed : 17.03 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.22), residues: 1306 helix: -0.60 (0.24), residues: 466 sheet: -2.69 (0.55), residues: 76 loop : -3.03 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.015 0.002 TYR A 824 PHE 0.016 0.002 PHE A 744 TRP 0.026 0.002 TRP B 524 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.26 (10494) covalent geometry : angle 0.65685 / 0.34 (14303) hydrogen bonds : bond 0.04746 / 3.16 ( 313) hydrogen bonds : angle 5.56253 / 3.90 ( 870) metal coordination : bond 0.02679 / 1.55 ( 24) metal coordination : angle 25.06556 / 16.16 ( 62) Misc. bond : bond 0.00091 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7761 (p) REVERT: A 119 MET cc_start: 0.8509 (mmm) cc_final: 0.8173 (mmm) REVERT: A 251 MET cc_start: 0.8316 (tmm) cc_final: 0.8009 (tmm) REVERT: A 594 MET cc_start: 0.6953 (mmp) cc_final: 0.6656 (mmt) outliers start: 21 outliers final: 18 residues processed: 122 average time/residue: 0.1745 time to fit residues: 32.0599 Evaluate side-chains 119 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.090699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.081729 restraints weight = 61340.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084282 restraints weight = 24320.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.085840 restraints weight = 11969.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086787 restraints weight = 6823.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087355 restraints weight = 4349.596| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10519 Z= 0.104 Angle : 1.623 62.247 14365 Z= 0.308 Chirality : 0.041 0.135 1569 Planarity : 0.004 0.049 1865 Dihedral : 7.194 179.246 1460 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.96 % Favored : 91.96 % Rotamer: Outliers : 1.24 % Allowed : 17.98 % Favored : 80.78 % 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: -2.56 (0.23), residues: 1306 helix: -0.30 (0.25), residues: 474 sheet: -2.19 (0.53), residues: 84 loop : -2.71 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 584 TYR 0.010 0.001 TYR A 315 PHE 0.016 0.001 PHE A 744 TRP 0.011 0.001 TRP A 197 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (10494) covalent geometry : angle 0.54620 / 0.28 (14303) hydrogen bonds : bond 0.03499 / 2.34 ( 313) hydrogen bonds : angle 5.18272 / 3.64 ( 870) metal coordination : bond 0.01117 / 0.65 ( 24) metal coordination : angle 23.27662 / 15.03 ( 62) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.28 seconds wall clock time: 46 minutes 30.88 seconds (2790.88 seconds total)