Starting phenix.real_space_refine on Thu Jul 2 22:48:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xqw_33402/07_2026/7xqw_33402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqw_33402/07_2026/7xqw_33402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2026/7xqw_33402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2026/7xqw_33402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2026/7xqw_33402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2026/7xqw_33402.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2026/7xqw_33402.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2026/7xqw_33402.cif" } resolution = 2.83 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= -0.004 sd= 0.416 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1 atoms to isotropic. 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: 7 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 6478 2.51 5 N 1847 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10391 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6070 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 46, 'TRANS': 743} Chain: "B" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4155 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 512} 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 2823 SG CYS A 436 38.796 41.161 97.901 1.00 30.06 S ATOM 265 SG CYS A 102 49.846 56.059 57.111 1.00 6.05 S ATOM 366 SG CYS A 115 50.188 58.413 56.214 1.00 5.19 S ATOM 388 SG CYS A 118 54.459 56.843 55.167 1.00 6.36 S ATOM 490 SG CYS A 132 53.154 54.080 57.928 1.00 6.68 S ATOM 1137 SG CYS A 216 44.284 58.289 60.773 1.00 5.04 S ATOM 1114 SG CYS A 213 37.999 59.406 59.077 1.00 4.73 S ATOM 1497 SG CYS A 266 41.040 61.341 64.716 1.00 4.47 S ATOM 1159 SG CYS A 219 39.339 55.080 63.198 1.00 4.82 S ATOM 1470 SG CYS A 262 38.075 55.629 69.657 1.00 4.49 S ATOM 1433 SG CYS A 256 33.221 53.159 72.467 1.00 7.86 S ATOM 1451 SG CYS A 259 39.131 51.450 74.442 1.00 4.94 S ATOM 1188 SG CYS A 223 37.224 49.225 68.875 1.00 5.66 S ATOM 1718 SG CYS A 295 42.563 54.021 86.838 1.00 10.97 S ATOM 1977 SG CYS A 329 39.198 50.941 82.741 1.00 6.79 S ATOM 1743 SG CYS A 298 40.939 48.104 86.685 1.00 11.58 S ATOM 1764 SG CYS A 302 45.768 51.518 82.517 1.00 10.15 S ATOM 10068 SG CYS B 542 45.532 49.480 43.520 1.00 6.26 S ATOM 9808 SG CYS B 508 42.415 54.946 43.829 1.00 5.94 S ATOM 9788 SG CYS B 505 46.218 54.628 47.560 1.00 5.57 S ATOM 9769 SG CYS B 502 41.464 49.903 48.254 1.00 5.50 S ATOM 6791 SG CYS B 113 28.519 49.098 31.049 1.00 15.72 S ATOM 6826 SG CYS B 118 27.173 48.927 27.718 1.00 16.89 S ATOM 7038 SG CYS B 146 32.281 46.333 30.942 1.00 13.72 S ATOM 7063 SG CYS B 150 32.668 46.254 27.160 1.00 17.32 S Time building chain proxies: 2.37, per 1000 atoms: 0.23 Number of scatterers: 10391 At special positions: 0 Unit cell: (85.32, 86.4, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) W 1 73.95 Fe 20 26.01 S 85 16.00 P 5 15.00 O 1955 8.00 N 1847 7.00 C 6478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 387.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1004 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 102 " pdb="FE1 FES A1004 " - pdb=" N HIS A 103 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 118 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 132 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 115 " pdb=" FES B 603 " pdb="FE1 FES B 603 " - pdb=" SG CYS B 113 " pdb="FE2 FES B 603 " - pdb=" SG CYS B 150 " pdb="FE1 FES B 603 " - pdb=" SG CYS B 118 " pdb="FE2 FES B 603 " - pdb=" SG CYS B 146 " pdb=" SF4 A1005 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 216 " pdb="FE4 SF4 A1005 " - pdb=" SG CYS A 219 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 213 " pdb="FE3 SF4 A1005 " - pdb=" SG CYS A 266 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 256 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 259 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 223 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 262 " pdb=" SF4 A1007 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 295 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 329 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 298 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 302 " pdb=" SF4 B 602 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 505 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 542 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 502 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 508 " Number of angles added : 62 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 45.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 146 through 164 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.688A pdb=" N CYS A 266 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.556A pdb=" N TYR A 338 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 removed outlier: 3.583A pdb=" N LEU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.801A pdb=" N LEU A 400 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 437 through 449 Processing helix chain 'A' and resid 456 through 462 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 503 through 509 removed outlier: 3.589A pdb=" N ARG A 507 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 removed outlier: 4.052A pdb=" N MET A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 545 removed outlier: 3.591A pdb=" N ILE A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 removed outlier: 4.050A pdb=" N LEU A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 removed outlier: 4.422A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 601 through 616 removed outlier: 4.205A pdb=" N ASN A 605 " --> pdb=" O HIS A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 641 Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 678 through 688 removed outlier: 3.803A pdb=" N HIS A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 793 through 803 Processing helix chain 'A' and resid 812 through 818 Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.689A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.601A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.529A pdb=" N LEU B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 3.810A pdb=" N PHE B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 removed outlier: 3.642A pdb=" N ALA B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 370 through 383 removed outlier: 3.594A pdb=" N TRP B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.871A pdb=" N TRP B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS B 390 " --> pdb=" O TRP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.523A pdb=" N TYR B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 501 Processing helix chain 'B' and resid 505 through 520 removed outlier: 3.994A pdb=" N GLN B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 Processing helix chain 'B' and resid 542 through 549 removed outlier: 4.448A pdb=" N SER B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 560 through 563 removed outlier: 3.625A pdb=" N PHE B 563 " --> pdb=" O PRO B 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.662A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 234 Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 293 removed outlier: 3.698A pdb=" N TYR A 315 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 512 removed outlier: 3.833A pdb=" N ARG A 511 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 466 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 465 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE A 591 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 467 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER A 588 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS A 627 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 590 " --> pdb=" O HIS A 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 752 Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 67 removed outlier: 6.413A pdb=" N ILE B 66 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 139 through 144 Processing sheet with id=AB3, first strand: chain 'B' and resid 319 through 324 removed outlier: 6.366A pdb=" N VAL B 291 " --> pdb=" O HIS B 321 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG B 323 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE B 293 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 250 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 366 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 411 through 416 removed outlier: 7.871A pdb=" N VAL B 477 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER B 402 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE B 479 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER B 404 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N SER B 481 " --> pdb=" O SER B 404 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4448 1.43 - 1.64: 6039 1.64 - 1.86: 99 1.86 - 2.07: 2 2.07 - 2.28: 56 Bond restraints: 10644 Sorted by residual: bond pdb=" C12 MGD A1002 " pdb=" C13 MGD A1002 " ideal model delta sigma weight residual 1.337 1.526 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C6 MGD A1002 " pdb=" O6 MGD A1002 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" C6 MGD A1003 " pdb=" O6 MGD A1003 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C12 MGD A1003 " pdb=" C13 MGD A1003 " ideal model delta sigma weight residual 1.337 1.519 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" C17 MGD A1002 " pdb=" O17 MGD A1002 " ideal model delta sigma weight residual 1.232 1.398 -0.166 2.00e-02 2.50e+03 6.87e+01 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 14404 3.43 - 6.85: 74 6.85 - 10.28: 20 10.28 - 13.71: 7 13.71 - 17.13: 6 Bond angle restraints: 14511 Sorted by residual: angle pdb=" C13 MGD A1003 " pdb=" C12 MGD A1003 " pdb=" S12 MGD A1003 " ideal model delta sigma weight residual 125.54 108.41 17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3A MGD A1003 " pdb=" PA MGD A1003 " pdb=" O3B MGD A1003 " ideal model delta sigma weight residual 93.37 109.82 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O3B MGD A1002 " pdb=" PB MGD A1002 " pdb=" O5' MGD A1002 " ideal model delta sigma weight residual 93.25 108.57 -15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C13 MGD A1002 " pdb=" C12 MGD A1002 " pdb=" S12 MGD A1002 " ideal model delta sigma weight residual 125.54 110.48 15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" O3A MGD A1002 " pdb=" PA MGD A1002 " pdb=" O3B MGD A1002 " ideal model delta sigma weight residual 93.37 108.03 -14.66 3.00e+00 1.11e-01 2.39e+01 ... (remaining 14506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 6142 32.85 - 65.71: 137 65.71 - 98.56: 11 98.56 - 131.41: 0 131.41 - 164.26: 2 Dihedral angle restraints: 6292 sinusoidal: 2496 harmonic: 3796 Sorted by residual: dihedral pdb=" C10 FMN B 601 " pdb=" C1' FMN B 601 " pdb=" N10 FMN B 601 " pdb=" C2' FMN B 601 " ideal model delta sinusoidal sigma weight residual 257.59 93.33 164.26 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" CA LYS B 351 " pdb=" C LYS B 351 " pdb=" N PRO B 352 " pdb=" CA PRO B 352 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" O5' MGD A1003 " pdb=" O3B MGD A1003 " pdb=" PB MGD A1003 " pdb=" PA MGD A1003 " ideal model delta sinusoidal sigma weight residual 203.73 43.28 160.45 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 6289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1479 0.087 - 0.174: 106 0.174 - 0.261: 4 0.261 - 0.348: 1 0.348 - 0.435: 3 Chirality restraints: 1593 Sorted by residual: chirality pdb=" C4' MGD A1003 " pdb=" C3' MGD A1003 " pdb=" C5' MGD A1003 " pdb=" O4' MGD A1003 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA ALA A 711 " pdb=" N ALA A 711 " pdb=" C ALA A 711 " pdb=" CB ALA A 711 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA GLU A 835 " pdb=" N GLU A 835 " pdb=" C GLU A 835 " pdb=" CB GLU A 835 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 1590 not shown) Planarity restraints: 1896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 MGD A1002 " 0.067 2.00e-02 2.50e+03 1.23e-01 4.14e+02 pdb=" C17 MGD A1002 " -0.008 2.00e-02 2.50e+03 pdb=" C19 MGD A1002 " -0.021 2.00e-02 2.50e+03 pdb=" C21 MGD A1002 " 0.094 2.00e-02 2.50e+03 pdb=" C23 MGD A1002 " -0.311 2.00e-02 2.50e+03 pdb=" N15 MGD A1002 " 0.110 2.00e-02 2.50e+03 pdb=" N18 MGD A1002 " -0.051 2.00e-02 2.50e+03 pdb=" N19 MGD A1002 " -0.067 2.00e-02 2.50e+03 pdb=" N20 MGD A1002 " 0.053 2.00e-02 2.50e+03 pdb=" N22 MGD A1002 " 0.176 2.00e-02 2.50e+03 pdb=" O17 MGD A1002 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' MGD A1003 " -0.093 2.00e-02 2.50e+03 3.53e-02 3.73e+01 pdb=" C2 MGD A1003 " 0.007 2.00e-02 2.50e+03 pdb=" C4 MGD A1003 " 0.026 2.00e-02 2.50e+03 pdb=" C5 MGD A1003 " 0.006 2.00e-02 2.50e+03 pdb=" C6 MGD A1003 " -0.016 2.00e-02 2.50e+03 pdb=" C8 MGD A1003 " 0.034 2.00e-02 2.50e+03 pdb=" N1 MGD A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N2 MGD A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N3 MGD A1003 " 0.025 2.00e-02 2.50e+03 pdb=" N7 MGD A1003 " 0.011 2.00e-02 2.50e+03 pdb=" N9 MGD A1003 " 0.043 2.00e-02 2.50e+03 pdb=" O6 MGD A1003 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 351 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO B 352 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 352 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 352 " 0.032 5.00e-02 4.00e+02 ... (remaining 1893 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 46 2.44 - 3.06: 7164 3.06 - 3.67: 16205 3.67 - 4.29: 25553 4.29 - 4.90: 41588 Nonbonded interactions: 90556 Sorted by model distance: nonbonded pdb=" OD2 ASP A 725 " pdb=" CG2 THR A 729 " model vdw 1.827 3.460 nonbonded pdb=" O2' FMN B 601 " pdb=" O4' FMN B 601 " model vdw 1.898 3.040 nonbonded pdb=" OD1 ASP A 725 " pdb=" N LEU A 726 " model vdw 2.154 3.120 nonbonded pdb=" OE1 GLN A 325 " pdb=" NH2 ARG A 327 " model vdw 2.204 3.120 nonbonded pdb=" O VAL A 479 " pdb=" OG1 THR A 482 " model vdw 2.211 3.040 ... (remaining 90551 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.008 0.189 10670 Z= 0.389 Angle : 1.127 41.255 14573 Z= 0.359 Chirality : 0.047 0.435 1593 Planarity : 0.006 0.123 1896 Dihedral : 14.635 164.263 3860 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.23), residues: 1327 helix: 0.50 (0.24), residues: 503 sheet: -0.08 (0.54), residues: 100 loop : -1.30 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 511 TYR 0.021 0.001 TYR A 824 PHE 0.013 0.001 PHE A 245 TRP 0.024 0.002 TRP B 524 HIS 0.011 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.37 (10644) covalent geometry : angle 0.79205 / 0.35 (14511) hydrogen bonds : bond 0.19381 / 12.96 ( 413) hydrogen bonds : angle 7.89389 / 5.66 ( 1134) metal coordination : bond 0.03505 / 1.74 ( 25) metal coordination : angle 12.32487 / 7.57 ( 62) Misc. bond : bond 0.12434 / 6.54 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.261 Fit side-chains REVERT: A 389 LYS cc_start: 0.7553 (tttm) cc_final: 0.7255 (tttt) REVERT: A 555 LYS cc_start: 0.7266 (ttpt) cc_final: 0.7017 (mtmp) REVERT: A 730 GLU cc_start: 0.7358 (mp0) cc_final: 0.7019 (mp0) REVERT: B 44 THR cc_start: 0.8119 (p) cc_final: 0.7892 (t) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.5295 time to fit residues: 106.2892 Evaluate side-chains 122 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.0170 chunk 55 optimal weight: 0.1980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS A 217 ASN A 428 ASN A 669 GLN A 720 HIS A 724 GLN A 734 HIS A 779 GLN A 810 ASN B 29 GLN B 273 HIS B 436 HIS B 492 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136445 restraints weight = 7685.823| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.14 r_work: 0.3517 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 10670 Z= 0.132 Angle : 1.012 40.390 14573 Z= 0.317 Chirality : 0.045 0.230 1593 Planarity : 0.005 0.070 1896 Dihedral : 7.726 157.436 1481 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.97 % Allowed : 11.24 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.23), residues: 1327 helix: 0.63 (0.23), residues: 515 sheet: -0.17 (0.51), residues: 104 loop : -1.16 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 660 TYR 0.019 0.001 TYR A 824 PHE 0.014 0.001 PHE B 162 TRP 0.011 0.001 TRP B 524 HIS 0.010 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10644) covalent geometry : angle 0.62865 / 0.31 (14511) hydrogen bonds : bond 0.04099 / 2.77 ( 413) hydrogen bonds : angle 5.81340 / 4.22 ( 1134) metal coordination : bond 0.03357 / 1.66 ( 25) metal coordination : angle 12.16916 / 7.44 ( 62) Misc. bond : bond 0.00131 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.391 Fit side-chains REVERT: A 389 LYS cc_start: 0.6930 (tttm) cc_final: 0.6453 (tttt) REVERT: A 437 HIS cc_start: 0.6704 (OUTLIER) cc_final: 0.5811 (m-70) REVERT: A 547 GLU cc_start: 0.7665 (mp0) cc_final: 0.7257 (mp0) REVERT: A 665 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7310 (tp30) REVERT: A 694 MET cc_start: 0.7104 (mtm) cc_final: 0.6868 (mtp) REVERT: A 730 GLU cc_start: 0.7209 (mp0) cc_final: 0.6855 (mp0) REVERT: B 44 THR cc_start: 0.8109 (p) cc_final: 0.7730 (t) REVERT: B 271 ASP cc_start: 0.8047 (t0) cc_final: 0.7721 (t70) REVERT: B 304 GLU cc_start: 0.7673 (tp30) cc_final: 0.7414 (tt0) REVERT: B 483 GLN cc_start: 0.7763 (mp10) cc_final: 0.7477 (mm110) REVERT: B 562 LEU cc_start: 0.7674 (mt) cc_final: 0.7464 (mt) outliers start: 21 outliers final: 10 residues processed: 153 average time/residue: 0.4997 time to fit residues: 82.5972 Evaluate side-chains 134 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 458 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 GLN A 724 GLN A 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127979 restraints weight = 7572.546| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.24 r_work: 0.3412 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 10670 Z= 0.136 Angle : 0.984 41.121 14573 Z= 0.306 Chirality : 0.045 0.203 1593 Planarity : 0.005 0.072 1896 Dihedral : 7.556 158.194 1481 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.28 % Allowed : 14.04 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1327 helix: 0.74 (0.23), residues: 515 sheet: -0.42 (0.48), residues: 117 loop : -1.15 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 660 TYR 0.019 0.001 TYR A 824 PHE 0.013 0.001 PHE A 245 TRP 0.014 0.001 TRP B 524 HIS 0.004 0.001 HIS A 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (10644) covalent geometry : angle 0.60819 / 0.30 (14511) hydrogen bonds : bond 0.03944 / 2.68 ( 413) hydrogen bonds : angle 5.52916 / 4.02 ( 1134) metal coordination : bond 0.03616 / 1.80 ( 25) metal coordination : angle 11.87829 / 7.21 ( 62) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.407 Fit side-chains REVERT: A 292 LYS cc_start: 0.7927 (ptmm) cc_final: 0.7666 (ttpt) REVERT: A 389 LYS cc_start: 0.6710 (tttm) cc_final: 0.6477 (tttt) REVERT: A 437 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.5812 (m-70) REVERT: A 490 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: A 491 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6275 (mmm-85) REVERT: A 547 GLU cc_start: 0.7311 (mp0) cc_final: 0.6967 (mp0) REVERT: A 581 LEU cc_start: 0.7588 (tp) cc_final: 0.7355 (tp) REVERT: A 586 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7704 (tttp) REVERT: A 665 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7300 (tp30) REVERT: A 694 MET cc_start: 0.7246 (mtm) cc_final: 0.7012 (mtp) REVERT: A 730 GLU cc_start: 0.7325 (mp0) cc_final: 0.6874 (mp0) REVERT: A 827 ASP cc_start: 0.6312 (OUTLIER) cc_final: 0.6104 (m-30) REVERT: B 44 THR cc_start: 0.8143 (p) cc_final: 0.7742 (t) REVERT: B 333 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: B 381 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6326 (pt0) REVERT: B 483 GLN cc_start: 0.7552 (mp10) cc_final: 0.7232 (mm110) outliers start: 35 outliers final: 12 residues processed: 158 average time/residue: 0.5139 time to fit residues: 87.8265 Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS A 203 HIS A 724 GLN A 734 HIS B 492 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125880 restraints weight = 7458.914| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.10 r_work: 0.3369 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 10670 Z= 0.167 Angle : 1.019 42.813 14573 Z= 0.322 Chirality : 0.046 0.199 1593 Planarity : 0.005 0.075 1896 Dihedral : 7.661 160.401 1481 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.31 % Allowed : 15.36 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.23), residues: 1327 helix: 0.51 (0.23), residues: 531 sheet: -0.44 (0.47), residues: 117 loop : -1.22 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 236 TYR 0.022 0.002 TYR A 824 PHE 0.016 0.002 PHE A 245 TRP 0.021 0.002 TRP B 524 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (10644) covalent geometry : angle 0.64489 / 0.31 (14511) hydrogen bonds : bond 0.04098 / 2.77 ( 413) hydrogen bonds : angle 5.54698 / 4.05 ( 1134) metal coordination : bond 0.04046 / 2.05 ( 25) metal coordination : angle 12.11723 / 7.28 ( 62) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 0.273 Fit side-chains REVERT: A 389 LYS cc_start: 0.6857 (tttm) cc_final: 0.6502 (tttt) REVERT: A 415 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 490 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: A 491 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6292 (mmm-85) REVERT: A 547 GLU cc_start: 0.7389 (mp0) cc_final: 0.7086 (mp0) REVERT: A 589 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7915 (tt) REVERT: A 665 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7290 (tp30) REVERT: A 694 MET cc_start: 0.7201 (mtm) cc_final: 0.6969 (mtp) REVERT: A 717 MET cc_start: 0.6738 (ttp) cc_final: 0.6537 (ttp) REVERT: A 730 GLU cc_start: 0.7467 (mp0) cc_final: 0.7060 (mp0) REVERT: A 810 ASN cc_start: 0.7490 (t0) cc_final: 0.7197 (t0) REVERT: B 44 THR cc_start: 0.8232 (p) cc_final: 0.7850 (t) REVERT: B 333 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: B 432 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6723 (mt) REVERT: B 483 GLN cc_start: 0.7590 (mp10) cc_final: 0.7255 (mm110) outliers start: 46 outliers final: 19 residues processed: 155 average time/residue: 0.4912 time to fit residues: 82.1933 Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A 431 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 = 0.3744 r_free = 0.3744 target = 0.151220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125127 restraints weight = 7114.803| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.18 r_work: 0.3391 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 10670 Z= 0.142 Angle : 0.998 43.949 14573 Z= 0.308 Chirality : 0.045 0.198 1593 Planarity : 0.005 0.074 1896 Dihedral : 7.545 158.586 1481 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.31 % Allowed : 16.20 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1327 helix: 0.62 (0.23), residues: 524 sheet: -0.47 (0.47), residues: 117 loop : -1.22 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 236 TYR 0.019 0.001 TYR A 824 PHE 0.014 0.001 PHE A 245 TRP 0.017 0.001 TRP B 524 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (10644) covalent geometry : angle 0.61647 / 0.30 (14511) hydrogen bonds : bond 0.03790 / 2.57 ( 413) hydrogen bonds : angle 5.47010 / 4.01 ( 1134) metal coordination : bond 0.03579 / 1.82 ( 25) metal coordination : angle 12.05680 / 7.20 ( 62) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.294 Fit side-chains REVERT: A 292 LYS cc_start: 0.7957 (tttm) cc_final: 0.7726 (ttpt) REVERT: A 389 LYS cc_start: 0.6740 (tttm) cc_final: 0.6478 (tttt) REVERT: A 490 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: A 491 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6293 (mmm-85) REVERT: A 547 GLU cc_start: 0.7232 (mp0) cc_final: 0.6957 (mp0) REVERT: A 589 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7902 (tt) REVERT: A 630 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6473 (mtt-85) REVERT: A 665 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7240 (tp30) REVERT: A 717 MET cc_start: 0.6761 (ttp) cc_final: 0.6533 (ttp) REVERT: A 730 GLU cc_start: 0.7388 (mp0) cc_final: 0.6962 (mp0) REVERT: A 810 ASN cc_start: 0.7477 (t0) cc_final: 0.7157 (t0) REVERT: B 44 THR cc_start: 0.8145 (p) cc_final: 0.7744 (t) REVERT: B 61 ASP cc_start: 0.8002 (m-30) cc_final: 0.7715 (m-30) REVERT: B 333 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7708 (tp30) REVERT: B 432 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6565 (mt) REVERT: B 483 GLN cc_start: 0.7522 (mp10) cc_final: 0.7189 (mm110) outliers start: 46 outliers final: 26 residues processed: 157 average time/residue: 0.5319 time to fit residues: 89.7441 Evaluate side-chains 140 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.0060 chunk 51 optimal weight: 5.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN A 724 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126461 restraints weight = 6720.292| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.12 r_work: 0.3414 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 10670 Z= 0.130 Angle : 0.954 43.937 14573 Z= 0.298 Chirality : 0.044 0.219 1593 Planarity : 0.005 0.074 1896 Dihedral : 7.460 157.496 1481 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.21 % Allowed : 16.85 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.23), residues: 1327 helix: 0.70 (0.23), residues: 524 sheet: -0.56 (0.47), residues: 117 loop : -1.20 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 236 TYR 0.015 0.001 TYR A 824 PHE 0.012 0.001 PHE A 245 TRP 0.015 0.001 TRP B 524 HIS 0.002 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10644) covalent geometry : angle 0.59728 / 0.29 (14511) hydrogen bonds : bond 0.03616 / 2.46 ( 413) hydrogen bonds : angle 5.38835 / 3.95 ( 1134) metal coordination : bond 0.03363 / 1.69 ( 25) metal coordination : angle 11.41517 / 6.83 ( 62) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.244 Fit side-chains REVERT: A 389 LYS cc_start: 0.6719 (tttm) cc_final: 0.6463 (tttt) REVERT: A 491 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6261 (mmm-85) REVERT: A 547 GLU cc_start: 0.7224 (mp0) cc_final: 0.6913 (mp0) REVERT: A 589 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 630 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6391 (mtt-85) REVERT: A 640 ASP cc_start: 0.7979 (m-30) cc_final: 0.7723 (m-30) REVERT: A 665 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7168 (tp30) REVERT: A 717 MET cc_start: 0.6792 (ttp) cc_final: 0.6582 (ttp) REVERT: A 730 GLU cc_start: 0.7391 (mp0) cc_final: 0.7007 (mp0) REVERT: A 805 MET cc_start: 0.6948 (mtt) cc_final: 0.6684 (mtt) REVERT: A 810 ASN cc_start: 0.7524 (t0) cc_final: 0.7183 (t0) REVERT: B 44 THR cc_start: 0.8201 (p) cc_final: 0.7813 (t) REVERT: B 87 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: B 333 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: B 432 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6580 (mt) REVERT: B 483 GLN cc_start: 0.7613 (mp10) cc_final: 0.7396 (mm110) outliers start: 45 outliers final: 25 residues processed: 154 average time/residue: 0.5355 time to fit residues: 88.9538 Evaluate side-chains 143 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 99 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125614 restraints weight = 6440.055| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.10 r_work: 0.3402 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 10670 Z= 0.143 Angle : 0.964 44.001 14573 Z= 0.307 Chirality : 0.045 0.196 1593 Planarity : 0.005 0.074 1896 Dihedral : 7.479 158.020 1481 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.40 % Allowed : 17.98 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1327 helix: 0.71 (0.23), residues: 523 sheet: -0.61 (0.47), residues: 117 loop : -1.23 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 236 TYR 0.019 0.001 TYR A 824 PHE 0.013 0.001 PHE A 245 TRP 0.017 0.001 TRP B 524 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (10644) covalent geometry : angle 0.61145 / 0.30 (14511) hydrogen bonds : bond 0.03749 / 2.56 ( 413) hydrogen bonds : angle 5.40327 / 3.95 ( 1134) metal coordination : bond 0.03568 / 1.81 ( 25) metal coordination : angle 11.45210 / 6.82 ( 62) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.303 Fit side-chains REVERT: A 389 LYS cc_start: 0.6748 (tttm) cc_final: 0.6494 (tttt) REVERT: A 415 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 490 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: A 491 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6291 (mmm-85) REVERT: A 547 GLU cc_start: 0.7215 (mp0) cc_final: 0.6881 (mp0) REVERT: A 589 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7918 (tt) REVERT: A 630 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6398 (mtt-85) REVERT: A 640 ASP cc_start: 0.8031 (m-30) cc_final: 0.7752 (m-30) REVERT: A 665 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7158 (tp30) REVERT: A 717 MET cc_start: 0.6815 (ttp) cc_final: 0.6593 (ttp) REVERT: A 730 GLU cc_start: 0.7425 (mp0) cc_final: 0.7058 (mp0) REVERT: A 805 MET cc_start: 0.6952 (mtt) cc_final: 0.6723 (mtt) REVERT: B 44 THR cc_start: 0.8178 (p) cc_final: 0.7795 (t) REVERT: B 61 ASP cc_start: 0.7978 (m-30) cc_final: 0.7643 (m-30) REVERT: B 87 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: B 333 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7677 (tp30) REVERT: B 432 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6571 (mt) REVERT: B 483 GLN cc_start: 0.7720 (mp10) cc_final: 0.7455 (mm110) outliers start: 47 outliers final: 29 residues processed: 154 average time/residue: 0.5143 time to fit residues: 84.8718 Evaluate side-chains 149 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 131 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 0.0870 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** A 431 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 = 0.3770 r_free = 0.3770 target = 0.153740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128886 restraints weight = 6208.229| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.07 r_work: 0.3445 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.003 0.140 10670 Z= 0.116 Angle : 0.941 43.560 14573 Z= 0.291 Chirality : 0.043 0.186 1593 Planarity : 0.005 0.073 1896 Dihedral : 7.381 156.446 1481 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.75 % Allowed : 19.10 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1327 helix: 0.83 (0.23), residues: 523 sheet: -0.76 (0.44), residues: 128 loop : -1.17 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 236 TYR 0.015 0.001 TYR A 824 PHE 0.012 0.001 PHE A 245 TRP 0.011 0.001 TRP B 524 HIS 0.002 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (10644) covalent geometry : angle 0.58018 / 0.28 (14511) hydrogen bonds : bond 0.03426 / 2.35 ( 413) hydrogen bonds : angle 5.29943 / 3.87 ( 1134) metal coordination : bond 0.03047 / 1.54 ( 25) metal coordination : angle 11.37694 / 6.76 ( 62) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.253 Fit side-chains REVERT: A 389 LYS cc_start: 0.6712 (tttm) cc_final: 0.6451 (tttt) REVERT: A 491 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6273 (mmm-85) REVERT: A 586 LYS cc_start: 0.7416 (ptmt) cc_final: 0.7028 (ptmm) REVERT: A 630 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6279 (mtt-85) REVERT: A 640 ASP cc_start: 0.8004 (m-30) cc_final: 0.7729 (m-30) REVERT: A 665 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7151 (tp30) REVERT: A 703 MET cc_start: 0.3835 (OUTLIER) cc_final: 0.3070 (ppp) REVERT: A 730 GLU cc_start: 0.7434 (mp0) cc_final: 0.7037 (mp0) REVERT: B 44 THR cc_start: 0.8048 (p) cc_final: 0.7662 (t) REVERT: B 61 ASP cc_start: 0.7947 (m-30) cc_final: 0.7677 (m-30) REVERT: B 87 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: B 110 ILE cc_start: 0.7851 (pt) cc_final: 0.7635 (tt) REVERT: B 139 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7009 (t) REVERT: B 385 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7267 (mt-10) REVERT: B 432 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6527 (mt) outliers start: 40 outliers final: 26 residues processed: 150 average time/residue: 0.5154 time to fit residues: 82.9602 Evaluate side-chains 146 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 131 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 0.0070 chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132284 restraints weight = 6517.546| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.07 r_work: 0.3488 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 10670 Z= 0.121 Angle : 0.944 43.227 14573 Z= 0.293 Chirality : 0.043 0.189 1593 Planarity : 0.005 0.073 1896 Dihedral : 7.380 157.004 1481 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.46 % Allowed : 19.48 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1327 helix: 0.88 (0.23), residues: 523 sheet: -0.69 (0.44), residues: 130 loop : -1.16 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 236 TYR 0.016 0.001 TYR A 824 PHE 0.011 0.001 PHE A 245 TRP 0.012 0.001 TRP B 524 HIS 0.002 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10644) covalent geometry : angle 0.58448 / 0.28 (14511) hydrogen bonds : bond 0.03429 / 2.34 ( 413) hydrogen bonds : angle 5.27686 / 3.85 ( 1134) metal coordination : bond 0.03121 / 1.57 ( 25) metal coordination : angle 11.37735 / 6.76 ( 62) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.239 Fit side-chains REVERT: A 389 LYS cc_start: 0.6916 (tttm) cc_final: 0.6642 (tttt) REVERT: A 490 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: A 491 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6336 (mmm-85) REVERT: A 630 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6255 (mtt-85) REVERT: A 640 ASP cc_start: 0.7964 (m-30) cc_final: 0.7726 (m-30) REVERT: A 665 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7204 (tp30) REVERT: A 703 MET cc_start: 0.3774 (OUTLIER) cc_final: 0.3054 (ppp) REVERT: A 730 GLU cc_start: 0.7545 (mp0) cc_final: 0.7197 (mp0) REVERT: B 44 THR cc_start: 0.8076 (p) cc_final: 0.7710 (t) REVERT: B 50 ASP cc_start: 0.7719 (t0) cc_final: 0.7498 (m-30) REVERT: B 61 ASP cc_start: 0.7967 (m-30) cc_final: 0.7619 (m-30) REVERT: B 139 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7030 (t) REVERT: B 221 ASP cc_start: 0.7123 (m-30) cc_final: 0.6903 (t70) REVERT: B 333 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: B 432 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6547 (mt) outliers start: 37 outliers final: 27 residues processed: 140 average time/residue: 0.4592 time to fit residues: 69.5565 Evaluate side-chains 142 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 50 optimal weight: 0.0270 chunk 55 optimal weight: 0.1980 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 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 = 0.3842 r_free = 0.3842 target = 0.159368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134470 restraints weight = 6579.441| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.08 r_work: 0.3575 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 10670 Z= 0.109 Angle : 0.939 43.042 14573 Z= 0.288 Chirality : 0.043 0.182 1593 Planarity : 0.005 0.073 1896 Dihedral : 7.340 156.211 1481 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.18 % Allowed : 19.76 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1327 helix: 0.93 (0.23), residues: 526 sheet: -0.66 (0.45), residues: 124 loop : -1.12 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 236 TYR 0.014 0.001 TYR A 824 PHE 0.011 0.001 PHE A 245 TRP 0.010 0.001 TRP A 592 HIS 0.002 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10644) covalent geometry : angle 0.57516 / 0.28 (14511) hydrogen bonds : bond 0.03230 / 2.22 ( 413) hydrogen bonds : angle 5.20405 / 3.79 ( 1134) metal coordination : bond 0.02836 / 1.41 ( 25) metal coordination : angle 11.39126 / 6.77 ( 62) Misc. bond : bond 0.00032 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.250 Fit side-chains REVERT: A 389 LYS cc_start: 0.6902 (tttm) cc_final: 0.6651 (tttt) REVERT: A 490 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: A 491 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6350 (mmm-85) REVERT: A 630 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6183 (mtt-85) REVERT: A 640 ASP cc_start: 0.7888 (m-30) cc_final: 0.7579 (m-30) REVERT: A 665 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7231 (tp30) REVERT: A 703 MET cc_start: 0.3677 (OUTLIER) cc_final: 0.2992 (ppp) REVERT: A 713 HIS cc_start: 0.6696 (t-90) cc_final: 0.6376 (t-170) REVERT: A 730 GLU cc_start: 0.7432 (mp0) cc_final: 0.7122 (mp0) REVERT: B 44 THR cc_start: 0.8115 (p) cc_final: 0.7752 (t) REVERT: B 50 ASP cc_start: 0.7652 (t0) cc_final: 0.7434 (m-30) REVERT: B 61 ASP cc_start: 0.7963 (m-30) cc_final: 0.7615 (m-30) REVERT: B 139 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.6999 (t) REVERT: B 432 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6588 (mt) outliers start: 34 outliers final: 27 residues processed: 141 average time/residue: 0.4943 time to fit residues: 75.3422 Evaluate side-chains 143 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 127 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 94 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 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 = 0.3831 r_free = 0.3831 target = 0.158525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134432 restraints weight = 6654.515| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.02 r_work: 0.3520 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 10670 Z= 0.114 Angle : 0.942 42.587 14573 Z= 0.292 Chirality : 0.043 0.184 1593 Planarity : 0.005 0.073 1896 Dihedral : 7.338 156.547 1481 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.28 % Allowed : 20.04 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1327 helix: 0.93 (0.23), residues: 526 sheet: -0.62 (0.45), residues: 124 loop : -1.09 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 236 TYR 0.015 0.001 TYR A 824 PHE 0.011 0.001 PHE A 245 TRP 0.009 0.001 TRP A 592 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10644) covalent geometry : angle 0.58282 / 0.28 (14511) hydrogen bonds : bond 0.03236 / 2.22 ( 413) hydrogen bonds : angle 5.18220 / 3.77 ( 1134) metal coordination : bond 0.02912 / 1.45 ( 25) metal coordination : angle 11.36169 / 6.77 ( 62) Misc. bond : bond 0.00033 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.74 seconds wall clock time: 51 minutes 56.90 seconds (3116.90 seconds total)