Starting phenix.real_space_refine on Mon Jul 28 21:47:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqw_33402/07_2025/7xqw_33402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqw_33402/07_2025/7xqw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2025/7xqw_33402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2025/7xqw_33402.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2025/7xqw_33402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqw_33402/07_2025/7xqw_33402.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.63, per 1000 atoms: 0.64 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: 2.70 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.47 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: 3.63 Time building geometry restraints manager: 3.11 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: 14394 3.43 - 6.85: 82 6.85 - 10.28: 22 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 - 32.09: 6208 32.09 - 64.18: 168 64.18 - 96.27: 23 96.27 - 128.36: 2 128.36 - 160.45: 1 Dihedral angle restraints: 6402 sinusoidal: 2606 harmonic: 3796 Sorted by residual: 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 dihedral pdb=" CA THR A 823 " pdb=" C THR A 823 " pdb=" N TYR A 824 " pdb=" CA TYR A 824 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6399 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: 1897 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 1894 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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= 0.400 Angle : 1.140 41.255 14573 Z= 0.364 Chirality : 0.047 0.435 1593 Planarity : 0.006 0.123 1897 Dihedral : 15.296 160.449 3970 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP B 524 HIS 0.011 0.001 HIS B 57 PHE 0.013 0.001 PHE A 245 TYR 0.021 0.001 TYR A 824 ARG 0.009 0.001 ARG A 511 Details of bonding type rmsd hydrogen bonds : bond 0.19381 ( 413) hydrogen bonds : angle 7.89389 ( 1134) metal coordination : bond 0.03505 ( 25) metal coordination : angle 12.32487 ( 62) covalent geometry : bond 0.00768 (10644) covalent geometry : angle 0.80933 (14511) Misc. bond : bond 0.12434 ( 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 : 1.162 Fit side-chains REVERT: A 389 LYS cc_start: 0.7553 (tttm) cc_final: 0.7256 (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: 1.4851 time to fit residues: 299.0795 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 : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 164 GLN A 217 ASN A 428 ASN A 669 GLN A 720 HIS A 724 GLN A 734 HIS A 810 ASN B 273 HIS B 492 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130654 restraints weight = 7180.408| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.12 r_work: 0.3460 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 10670 Z= 0.159 Angle : 1.044 41.108 14573 Z= 0.337 Chirality : 0.047 0.190 1593 Planarity : 0.005 0.072 1897 Dihedral : 9.534 157.251 1591 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.43 % Allowed : 11.33 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1327 helix: 0.49 (0.23), residues: 515 sheet: -0.22 (0.51), residues: 104 loop : -1.20 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 524 HIS 0.009 0.001 HIS A 713 PHE 0.013 0.002 PHE A 245 TYR 0.022 0.002 TYR A 824 ARG 0.007 0.001 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 413) hydrogen bonds : angle 5.89276 ( 1134) metal coordination : bond 0.03995 ( 25) metal coordination : angle 12.29453 ( 62) covalent geometry : bond 0.00374 (10644) covalent geometry : angle 0.66968 (14511) Misc. bond : bond 0.00014 ( 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 167 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.101 Fit side-chains REVERT: A 389 LYS cc_start: 0.6940 (tttm) cc_final: 0.6452 (tttt) REVERT: A 437 HIS cc_start: 0.6903 (OUTLIER) cc_final: 0.6080 (m-70) REVERT: A 490 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: A 555 LYS cc_start: 0.7004 (ttpt) cc_final: 0.6008 (mtmp) REVERT: A 665 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7328 (tp30) REVERT: A 694 MET cc_start: 0.7191 (mtm) cc_final: 0.6933 (mtp) REVERT: A 730 GLU cc_start: 0.7354 (mp0) cc_final: 0.6925 (mp0) REVERT: B 44 THR cc_start: 0.8237 (p) cc_final: 0.7868 (t) REVERT: B 304 GLU cc_start: 0.7635 (tp30) cc_final: 0.7346 (tt0) REVERT: B 333 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7580 (tp30) REVERT: B 483 GLN cc_start: 0.7664 (mp10) cc_final: 0.7375 (mm110) REVERT: B 562 LEU cc_start: 0.7771 (mt) cc_final: 0.7530 (mt) outliers start: 26 outliers final: 11 residues processed: 152 average time/residue: 1.4098 time to fit residues: 230.5551 Evaluate side-chains 139 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 440 SER Chi-restraints excluded: chain A residue 490 GLN 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 218 VAL Chi-restraints excluded: chain B residue 333 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.0670 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 203 HIS A 724 GLN A 810 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126287 restraints weight = 6547.696| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.12 r_work: 0.3392 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 10670 Z= 0.150 Angle : 1.007 43.032 14573 Z= 0.316 Chirality : 0.045 0.195 1593 Planarity : 0.005 0.074 1897 Dihedral : 8.896 145.627 1591 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.03 % Allowed : 13.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1327 helix: 0.48 (0.23), residues: 523 sheet: -0.41 (0.47), residues: 117 loop : -1.22 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 524 HIS 0.004 0.001 HIS B 55 PHE 0.016 0.001 PHE A 245 TYR 0.021 0.002 TYR A 824 ARG 0.008 0.001 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 413) hydrogen bonds : angle 5.60860 ( 1134) metal coordination : bond 0.03755 ( 25) metal coordination : angle 12.08370 ( 62) covalent geometry : bond 0.00354 (10644) covalent geometry : angle 0.62817 (14511) Misc. bond : bond 0.00064 ( 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 178 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 1.053 Fit side-chains REVERT: A 389 LYS cc_start: 0.6787 (tttm) cc_final: 0.6553 (tttt) REVERT: A 415 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7801 (mp) REVERT: A 437 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.5832 (m-70) REVERT: A 490 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: A 491 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6241 (mmm-85) REVERT: A 665 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7358 (tp30) REVERT: A 694 MET cc_start: 0.7161 (mtm) cc_final: 0.6953 (mtp) REVERT: A 730 GLU cc_start: 0.7323 (mp0) cc_final: 0.6910 (mp0) REVERT: B 44 THR cc_start: 0.8229 (p) cc_final: 0.7846 (t) REVERT: B 61 ASP cc_start: 0.7949 (m-30) cc_final: 0.7620 (m-30) REVERT: B 319 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6919 (ptt90) REVERT: B 483 GLN cc_start: 0.7589 (mp10) cc_final: 0.7253 (mm110) REVERT: B 562 LEU cc_start: 0.7733 (mt) cc_final: 0.7528 (mt) outliers start: 43 outliers final: 18 residues processed: 160 average time/residue: 1.2291 time to fit residues: 212.2670 Evaluate side-chains 147 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 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 A residue 787 LEU 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 454 SER Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 81 optimal weight: 0.0980 chunk 122 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN A 724 GLN A 810 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121754 restraints weight = 6304.618| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.95 r_work: 0.3320 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.223 10670 Z= 0.264 Angle : 1.108 44.916 14573 Z= 0.380 Chirality : 0.051 0.234 1593 Planarity : 0.006 0.076 1897 Dihedral : 8.998 142.320 1591 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.15 % Allowed : 14.23 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1327 helix: 0.12 (0.22), residues: 521 sheet: -0.57 (0.46), residues: 117 loop : -1.41 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 524 HIS 0.005 0.001 HIS B 55 PHE 0.019 0.002 PHE A 245 TYR 0.029 0.002 TYR A 824 ARG 0.006 0.001 ARG B 406 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 413) hydrogen bonds : angle 5.86212 ( 1134) metal coordination : bond 0.05008 ( 25) metal coordination : angle 12.33415 ( 62) covalent geometry : bond 0.00641 (10644) covalent geometry : angle 0.76289 (14511) Misc. bond : bond 0.00059 ( 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 173 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 1.130 Fit side-chains REVERT: A 389 LYS cc_start: 0.6968 (tttm) cc_final: 0.6542 (tttt) REVERT: A 415 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8107 (mp) REVERT: A 490 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: A 491 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6316 (mmm-85) REVERT: A 571 ASP cc_start: 0.6271 (m-30) cc_final: 0.5979 (m-30) REVERT: A 589 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 630 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6515 (mtt-85) REVERT: A 665 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7244 (tp30) REVERT: A 730 GLU cc_start: 0.7691 (mp0) cc_final: 0.7115 (mp0) REVERT: B 44 THR cc_start: 0.8292 (p) cc_final: 0.7934 (t) REVERT: B 61 ASP cc_start: 0.8034 (m-30) cc_final: 0.7540 (m-30) REVERT: B 333 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: B 483 GLN cc_start: 0.7733 (mp10) cc_final: 0.7228 (mm110) REVERT: B 562 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7713 (mt) outliers start: 55 outliers final: 26 residues processed: 160 average time/residue: 1.2281 time to fit residues: 212.4922 Evaluate side-chains 139 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 282 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 346 THR 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 444 LEU 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 A residue 787 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 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 121 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123797 restraints weight = 6004.308| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.06 r_work: 0.3347 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 10670 Z= 0.182 Angle : 1.014 45.923 14573 Z= 0.334 Chirality : 0.047 0.200 1593 Planarity : 0.005 0.074 1897 Dihedral : 8.775 139.541 1591 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.96 % Allowed : 15.36 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1327 helix: 0.25 (0.22), residues: 528 sheet: -0.66 (0.46), residues: 117 loop : -1.43 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 524 HIS 0.004 0.001 HIS A 176 PHE 0.017 0.002 PHE A 245 TYR 0.022 0.002 TYR A 824 ARG 0.008 0.001 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 413) hydrogen bonds : angle 5.68662 ( 1134) metal coordination : bond 0.03966 ( 25) metal coordination : angle 11.70794 ( 62) covalent geometry : bond 0.00438 (10644) covalent geometry : angle 0.66850 (14511) Misc. bond : bond 0.00056 ( 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 179 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 1.040 Fit side-chains REVERT: A 389 LYS cc_start: 0.6853 (tttm) cc_final: 0.6445 (tttt) REVERT: A 415 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 490 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: A 491 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6241 (mmm-85) REVERT: A 501 ARG cc_start: 0.7705 (mmt90) cc_final: 0.7489 (mmt-90) REVERT: A 547 GLU cc_start: 0.7324 (mp0) cc_final: 0.7033 (mp0) REVERT: A 589 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7883 (tt) REVERT: A 630 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6457 (mtt-85) REVERT: A 665 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7165 (tp30) REVERT: A 730 GLU cc_start: 0.7572 (mp0) cc_final: 0.7019 (mp0) REVERT: B 44 THR cc_start: 0.8251 (p) cc_final: 0.7888 (t) REVERT: B 61 ASP cc_start: 0.8071 (m-30) cc_final: 0.7636 (m-30) REVERT: B 87 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: B 333 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: B 432 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6584 (mm) REVERT: B 466 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: B 483 GLN cc_start: 0.7638 (mp10) cc_final: 0.7326 (mm110) REVERT: B 562 LEU cc_start: 0.7959 (mt) cc_final: 0.7725 (mt) outliers start: 53 outliers final: 27 residues processed: 165 average time/residue: 1.3667 time to fit residues: 242.8414 Evaluate side-chains 153 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 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 444 LEU 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 A residue 786 ASP 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 466 GLU 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 18 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125539 restraints weight = 5974.068| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.04 r_work: 0.3390 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 10670 Z= 0.137 Angle : 0.981 45.698 14573 Z= 0.308 Chirality : 0.045 0.227 1593 Planarity : 0.005 0.074 1897 Dihedral : 8.514 134.292 1591 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.78 % Allowed : 16.57 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1327 helix: 0.49 (0.23), residues: 527 sheet: -0.64 (0.46), residues: 117 loop : -1.36 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 524 HIS 0.003 0.001 HIS B 152 PHE 0.015 0.001 PHE A 245 TYR 0.017 0.001 TYR A 824 ARG 0.009 0.001 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 413) hydrogen bonds : angle 5.51650 ( 1134) metal coordination : bond 0.03352 ( 25) metal coordination : angle 11.75119 ( 62) covalent geometry : bond 0.00323 (10644) covalent geometry : angle 0.61309 (14511) Misc. bond : bond 0.00053 ( 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 172 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 1.186 Fit side-chains REVERT: A 389 LYS cc_start: 0.6822 (tttm) cc_final: 0.6547 (tttt) REVERT: A 415 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7868 (mp) REVERT: A 490 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: A 491 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6307 (mmm-85) REVERT: A 501 ARG cc_start: 0.7692 (mmt90) cc_final: 0.7478 (mmt-90) REVERT: A 547 GLU cc_start: 0.7306 (mp0) cc_final: 0.6896 (mp0) REVERT: A 589 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8001 (tt) REVERT: A 630 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6393 (mtt-85) REVERT: A 640 ASP cc_start: 0.8037 (m-30) cc_final: 0.7782 (m-30) REVERT: A 665 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7169 (tp30) REVERT: A 730 GLU cc_start: 0.7523 (mp0) cc_final: 0.7072 (mp0) REVERT: A 805 MET cc_start: 0.7106 (mtt) cc_final: 0.6888 (mtt) REVERT: B 44 THR cc_start: 0.8232 (p) cc_final: 0.7866 (t) REVERT: B 61 ASP cc_start: 0.8057 (m-30) cc_final: 0.7614 (m-30) REVERT: B 87 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: B 319 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6967 (ptt90) REVERT: B 432 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6496 (mm) REVERT: B 466 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6336 (mp0) REVERT: B 483 GLN cc_start: 0.7760 (mp10) cc_final: 0.7486 (mm110) REVERT: B 562 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7684 (mt) outliers start: 51 outliers final: 25 residues processed: 162 average time/residue: 1.2484 time to fit residues: 218.5400 Evaluate side-chains 148 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 282 THR 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 444 LEU 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 87 GLU 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 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 466 GLU Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN B 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122185 restraints weight = 6052.027| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.00 r_work: 0.3345 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 10670 Z= 0.200 Angle : 1.025 45.545 14573 Z= 0.341 Chirality : 0.048 0.228 1593 Planarity : 0.005 0.075 1897 Dihedral : 8.742 128.858 1591 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.43 % Allowed : 15.82 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1327 helix: 0.36 (0.22), residues: 528 sheet: -0.69 (0.45), residues: 119 loop : -1.41 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 524 HIS 0.004 0.001 HIS A 477 PHE 0.015 0.002 PHE A 245 TYR 0.024 0.002 TYR A 824 ARG 0.007 0.001 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 413) hydrogen bonds : angle 5.64334 ( 1134) metal coordination : bond 0.04207 ( 25) metal coordination : angle 11.76651 ( 62) covalent geometry : bond 0.00483 (10644) covalent geometry : angle 0.68022 (14511) Misc. bond : bond 0.00046 ( 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 169 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 1.147 Fit side-chains REVERT: A 415 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8020 (mp) REVERT: A 437 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.5487 (m90) REVERT: A 490 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: A 491 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6332 (mmm-85) REVERT: A 547 GLU cc_start: 0.7330 (mp0) cc_final: 0.7019 (mp0) REVERT: A 589 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7974 (tt) REVERT: A 630 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6453 (mtt-85) REVERT: A 665 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7208 (tp30) REVERT: A 713 HIS cc_start: 0.6810 (t-90) cc_final: 0.6454 (t-170) REVERT: A 730 GLU cc_start: 0.7624 (mp0) cc_final: 0.7135 (mp0) REVERT: B 44 THR cc_start: 0.8182 (p) cc_final: 0.7829 (t) REVERT: B 61 ASP cc_start: 0.8070 (m-30) cc_final: 0.7647 (m-30) REVERT: B 87 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: B 432 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6544 (mm) REVERT: B 466 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: B 483 GLN cc_start: 0.7633 (mp10) cc_final: 0.7329 (mm110) REVERT: B 562 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7765 (mt) outliers start: 58 outliers final: 28 residues processed: 155 average time/residue: 1.5661 time to fit residues: 262.2192 Evaluate side-chains 147 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 132 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 282 THR 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 437 HIS 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 A residue 804 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 137 ASP 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 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 466 GLU Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 85 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 90 optimal weight: 0.0870 chunk 122 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 77 optimal weight: 0.3980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN B 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126713 restraints weight = 5939.781| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.05 r_work: 0.3416 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 10670 Z= 0.118 Angle : 0.952 45.503 14573 Z= 0.294 Chirality : 0.043 0.185 1593 Planarity : 0.005 0.073 1897 Dihedral : 8.616 125.821 1591 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.31 % Allowed : 17.32 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1327 helix: 0.68 (0.23), residues: 522 sheet: -0.87 (0.44), residues: 128 loop : -1.32 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.003 0.001 HIS B 164 PHE 0.013 0.001 PHE A 245 TYR 0.014 0.001 TYR B 92 ARG 0.009 0.001 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 413) hydrogen bonds : angle 5.39543 ( 1134) metal coordination : bond 0.02987 ( 25) metal coordination : angle 11.56676 ( 62) covalent geometry : bond 0.00273 (10644) covalent geometry : angle 0.58242 (14511) Misc. bond : bond 0.00047 ( 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 173 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 1.428 Fit side-chains REVERT: A 415 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7815 (mp) REVERT: A 437 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.5255 (m90) REVERT: A 490 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: A 491 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6275 (mmm-85) REVERT: A 547 GLU cc_start: 0.7266 (mp0) cc_final: 0.6979 (mp0) REVERT: A 630 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6355 (mtt-85) REVERT: A 640 ASP cc_start: 0.7898 (m-30) cc_final: 0.7611 (m-30) REVERT: A 665 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7182 (tp30) REVERT: A 713 HIS cc_start: 0.6690 (t-90) cc_final: 0.6293 (t-170) REVERT: A 730 GLU cc_start: 0.7410 (mp0) cc_final: 0.6965 (mp0) REVERT: B 44 THR cc_start: 0.8148 (p) cc_final: 0.7787 (t) REVERT: B 61 ASP cc_start: 0.8004 (m-30) cc_final: 0.7579 (m-30) REVERT: B 87 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: B 319 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6838 (ptt90) REVERT: B 432 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6449 (mt) REVERT: B 483 GLN cc_start: 0.7660 (mp10) cc_final: 0.7401 (mm110) outliers start: 46 outliers final: 22 residues processed: 158 average time/residue: 1.3555 time to fit residues: 230.3341 Evaluate side-chains 140 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 132 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 444 LEU 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 46 optimal weight: 4.9990 chunk 70 optimal weight: 0.0870 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125623 restraints weight = 6078.629| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.05 r_work: 0.3403 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 10670 Z= 0.136 Angle : 0.974 45.029 14573 Z= 0.306 Chirality : 0.044 0.185 1593 Planarity : 0.005 0.075 1897 Dihedral : 8.570 121.435 1591 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.84 % Allowed : 18.26 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1327 helix: 0.71 (0.23), residues: 521 sheet: -0.70 (0.46), residues: 117 loop : -1.29 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 524 HIS 0.003 0.001 HIS B 152 PHE 0.014 0.001 PHE A 245 TYR 0.017 0.001 TYR A 824 ARG 0.009 0.000 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 413) hydrogen bonds : angle 5.38400 ( 1134) metal coordination : bond 0.03297 ( 25) metal coordination : angle 11.70218 ( 62) covalent geometry : bond 0.00322 (10644) covalent geometry : angle 0.60702 (14511) Misc. bond : bond 0.00048 ( 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 159 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 3.285 Fit side-chains REVERT: A 437 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.5358 (m90) REVERT: A 490 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: A 491 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.6288 (mmm-85) REVERT: A 589 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7922 (tt) REVERT: A 630 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6363 (mtt-85) REVERT: A 640 ASP cc_start: 0.7861 (m-30) cc_final: 0.7509 (m-30) REVERT: A 665 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7201 (tp30) REVERT: A 703 MET cc_start: 0.3333 (ttm) cc_final: 0.2720 (ppp) REVERT: A 713 HIS cc_start: 0.6651 (t-90) cc_final: 0.6282 (t-170) REVERT: A 730 GLU cc_start: 0.7434 (mp0) cc_final: 0.7005 (mp0) REVERT: B 44 THR cc_start: 0.8153 (p) cc_final: 0.7789 (t) REVERT: B 61 ASP cc_start: 0.7986 (m-30) cc_final: 0.7579 (m-30) REVERT: B 87 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: B 319 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7004 (ptt90) REVERT: B 385 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7148 (mt-10) REVERT: B 432 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6455 (mt) REVERT: B 483 GLN cc_start: 0.7653 (mp10) cc_final: 0.7378 (mm110) outliers start: 41 outliers final: 27 residues processed: 147 average time/residue: 1.7048 time to fit residues: 271.1171 Evaluate side-chains 144 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 132 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 282 THR 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 437 HIS Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 444 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 9 optimal weight: 0.7980 chunk 111 optimal weight: 0.0570 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127571 restraints weight = 6047.810| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.06 r_work: 0.3426 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 10670 Z= 0.121 Angle : 0.961 44.800 14573 Z= 0.298 Chirality : 0.044 0.190 1593 Planarity : 0.005 0.074 1897 Dihedral : 8.502 119.343 1591 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.18 % Allowed : 19.48 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1327 helix: 0.76 (0.23), residues: 521 sheet: -0.87 (0.44), residues: 128 loop : -1.19 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.003 0.001 HIS B 164 PHE 0.014 0.001 PHE A 245 TYR 0.016 0.001 TYR A 824 ARG 0.009 0.001 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 413) hydrogen bonds : angle 5.31640 ( 1134) metal coordination : bond 0.02967 ( 25) metal coordination : angle 11.66687 ( 62) covalent geometry : bond 0.00283 (10644) covalent geometry : angle 0.58833 (14511) Misc. bond : bond 0.00048 ( 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 152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.169 Fit side-chains REVERT: A 206 MET cc_start: 0.8078 (ptt) cc_final: 0.7795 (mtm) REVERT: A 437 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.5266 (m90) REVERT: A 490 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: A 491 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6288 (mmm-85) REVERT: A 630 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6332 (mtt-85) REVERT: A 640 ASP cc_start: 0.7847 (m-30) cc_final: 0.7515 (m-30) REVERT: A 665 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7197 (tp30) REVERT: A 703 MET cc_start: 0.3321 (ttm) cc_final: 0.2723 (ppp) REVERT: A 713 HIS cc_start: 0.6624 (t-90) cc_final: 0.6239 (t-170) REVERT: A 730 GLU cc_start: 0.7430 (mp0) cc_final: 0.7030 (mp0) REVERT: B 44 THR cc_start: 0.8078 (p) cc_final: 0.7699 (t) REVERT: B 61 ASP cc_start: 0.7943 (m-30) cc_final: 0.7507 (m-30) REVERT: B 87 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: B 319 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6724 (ptt90) REVERT: B 385 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6940 (mt-10) REVERT: B 432 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6507 (mt) REVERT: B 483 GLN cc_start: 0.7669 (mp10) cc_final: 0.7448 (mm110) outliers start: 34 outliers final: 27 residues processed: 143 average time/residue: 1.5100 time to fit residues: 233.8463 Evaluate side-chains 145 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 132 CYS 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 437 HIS Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 444 LEU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 115 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127086 restraints weight = 6041.589| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.05 r_work: 0.3418 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.141 10670 Z= 0.127 Angle : 0.964 44.686 14573 Z= 0.300 Chirality : 0.044 0.199 1593 Planarity : 0.005 0.074 1897 Dihedral : 8.505 117.825 1591 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.65 % Allowed : 18.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1327 helix: 0.77 (0.23), residues: 521 sheet: -0.85 (0.45), residues: 122 loop : -1.20 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 592 HIS 0.003 0.001 HIS B 164 PHE 0.014 0.001 PHE A 245 TYR 0.017 0.001 TYR A 824 ARG 0.009 0.000 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 413) hydrogen bonds : angle 5.30936 ( 1134) metal coordination : bond 0.03075 ( 25) metal coordination : angle 11.65049 ( 62) covalent geometry : bond 0.00298 (10644) covalent geometry : angle 0.59372 (14511) Misc. bond : bond 0.00045 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8180.74 seconds wall clock time: 146 minutes 29.47 seconds (8789.47 seconds total)