Starting phenix.real_space_refine on Fri Feb 14 22:31:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqw_33402/02_2025/7xqw_33402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqw_33402/02_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_33402/02_2025/7xqw_33402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqw_33402/02_2025/7xqw_33402.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqw_33402/02_2025/7xqw_33402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqw_33402/02_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-5592/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: 6.04, per 1000 atoms: 0.58 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: 2.90 Conformation dependent library (CDL) restraints added in 1.6 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: 1.25 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: 3.89 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4448 1.43 - 1.64: 6039 1.64 - 1.86: 99 1.86 - 2.07: 2 2.07 - 2.28: 56 Bond restraints: 10644 Sorted by residual: bond pdb=" C12 MGD A1002 " pdb=" C13 MGD A1002 " ideal model delta sigma weight residual 1.337 1.526 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C6 MGD A1002 " pdb=" O6 MGD A1002 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" C6 MGD A1003 " pdb=" O6 MGD A1003 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C12 MGD A1003 " pdb=" C13 MGD A1003 " ideal model delta sigma weight residual 1.337 1.519 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" C17 MGD A1002 " pdb=" O17 MGD A1002 " ideal model delta sigma weight residual 1.232 1.398 -0.166 2.00e-02 2.50e+03 6.87e+01 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 14404 3.43 - 6.85: 74 6.85 - 10.28: 20 10.28 - 13.71: 7 13.71 - 17.13: 6 Bond angle restraints: 14511 Sorted by residual: angle pdb=" C13 MGD A1003 " pdb=" C12 MGD A1003 " pdb=" S12 MGD A1003 " ideal model delta sigma weight residual 125.54 108.41 17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3A MGD A1003 " pdb=" PA MGD A1003 " pdb=" O3B MGD A1003 " ideal model delta sigma weight residual 93.37 109.82 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O3B MGD A1002 " pdb=" PB MGD A1002 " pdb=" O5' MGD A1002 " ideal model delta sigma weight residual 93.25 108.57 -15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C13 MGD A1002 " pdb=" C12 MGD A1002 " pdb=" S12 MGD A1002 " ideal model delta sigma weight residual 125.54 110.48 15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" O3A MGD A1002 " pdb=" PA MGD A1002 " pdb=" O3B MGD A1002 " ideal model delta sigma weight residual 93.37 108.03 -14.66 3.00e+00 1.11e-01 2.39e+01 ... (remaining 14506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 6216 32.85 - 65.71: 162 65.71 - 98.56: 19 98.56 - 131.41: 1 131.41 - 164.26: 2 Dihedral angle restraints: 6400 sinusoidal: 2604 harmonic: 3796 Sorted by residual: dihedral pdb=" C10 FMN B 601 " pdb=" C1' FMN B 601 " pdb=" N10 FMN B 601 " pdb=" C2' FMN B 601 " ideal model delta sinusoidal sigma weight residual 257.59 93.33 164.26 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" CA LYS B 351 " pdb=" C LYS B 351 " pdb=" N PRO B 352 " pdb=" CA PRO B 352 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" O5' MGD A1003 " pdb=" O3B MGD A1003 " pdb=" PB MGD A1003 " pdb=" PA MGD A1003 " ideal model delta sinusoidal sigma weight residual 203.73 43.28 160.45 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 6397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1479 0.087 - 0.174: 106 0.174 - 0.261: 4 0.261 - 0.348: 1 0.348 - 0.435: 3 Chirality restraints: 1593 Sorted by residual: chirality pdb=" C4' MGD A1003 " pdb=" C3' MGD A1003 " pdb=" C5' MGD A1003 " pdb=" O4' MGD A1003 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA ALA A 711 " pdb=" N ALA A 711 " pdb=" C ALA A 711 " pdb=" CB ALA A 711 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA GLU A 835 " pdb=" N GLU A 835 " pdb=" C GLU A 835 " pdb=" CB GLU A 835 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 1590 not shown) Planarity restraints: 1896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 MGD A1002 " 0.067 2.00e-02 2.50e+03 1.23e-01 4.14e+02 pdb=" C17 MGD A1002 " -0.008 2.00e-02 2.50e+03 pdb=" C19 MGD A1002 " -0.021 2.00e-02 2.50e+03 pdb=" C21 MGD A1002 " 0.094 2.00e-02 2.50e+03 pdb=" C23 MGD A1002 " -0.311 2.00e-02 2.50e+03 pdb=" N15 MGD A1002 " 0.110 2.00e-02 2.50e+03 pdb=" N18 MGD A1002 " -0.051 2.00e-02 2.50e+03 pdb=" N19 MGD A1002 " -0.067 2.00e-02 2.50e+03 pdb=" N20 MGD A1002 " 0.053 2.00e-02 2.50e+03 pdb=" N22 MGD A1002 " 0.176 2.00e-02 2.50e+03 pdb=" O17 MGD A1002 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' MGD A1003 " -0.093 2.00e-02 2.50e+03 3.53e-02 3.73e+01 pdb=" C2 MGD A1003 " 0.007 2.00e-02 2.50e+03 pdb=" C4 MGD A1003 " 0.026 2.00e-02 2.50e+03 pdb=" C5 MGD A1003 " 0.006 2.00e-02 2.50e+03 pdb=" C6 MGD A1003 " -0.016 2.00e-02 2.50e+03 pdb=" C8 MGD A1003 " 0.034 2.00e-02 2.50e+03 pdb=" N1 MGD A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N2 MGD A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N3 MGD A1003 " 0.025 2.00e-02 2.50e+03 pdb=" N7 MGD A1003 " 0.011 2.00e-02 2.50e+03 pdb=" N9 MGD A1003 " 0.043 2.00e-02 2.50e+03 pdb=" O6 MGD A1003 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 351 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO B 352 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 352 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 352 " 0.032 5.00e-02 4.00e+02 ... (remaining 1893 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 46 2.44 - 3.06: 7164 3.06 - 3.67: 16205 3.67 - 4.29: 25553 4.29 - 4.90: 41588 Nonbonded interactions: 90556 Sorted by model distance: nonbonded pdb=" OD2 ASP A 725 " pdb=" CG2 THR A 729 " model vdw 1.827 3.460 nonbonded pdb=" O2' FMN B 601 " pdb=" O4' FMN B 601 " model vdw 1.898 3.040 nonbonded pdb=" OD1 ASP A 725 " pdb=" N LEU A 726 " model vdw 2.154 3.120 nonbonded pdb=" OE1 GLN A 325 " pdb=" NH2 ARG A 327 " model vdw 2.204 3.120 nonbonded pdb=" O VAL A 479 " pdb=" OG1 THR A 482 " model vdw 2.211 3.040 ... (remaining 90551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.350 Find NCS groups from input model: 0.100 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:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- 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 : 0.007 0.189 10644 Z= 0.464 Angle : 0.792 17.134 14511 Z= 0.350 Chirality : 0.047 0.435 1593 Planarity : 0.006 0.123 1896 Dihedral : 15.553 164.263 3968 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 *********************** 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 : 1.199 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: 1.3134 time to fit residues: 264.2281 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 : 1.233 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.6980 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: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.155821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132247 restraints weight = 7159.497| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.06 r_work: 0.3468 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10644 Z= 0.243 Angle : 0.662 10.711 14511 Z= 0.323 Chirality : 0.047 0.188 1593 Planarity : 0.005 0.071 1896 Dihedral : 10.403 159.271 1589 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.53 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: -0.66 (0.23), residues: 1327 helix: 0.51 (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 0.010 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 B 236 *********************** 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 169 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.058 Fit side-chains REVERT: A 389 LYS cc_start: 0.6969 (tttm) cc_final: 0.6482 (tttt) REVERT: A 437 HIS cc_start: 0.6890 (OUTLIER) cc_final: 0.6069 (m-70) REVERT: A 490 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: A 665 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7332 (tp30) REVERT: A 694 MET cc_start: 0.7190 (mtm) cc_final: 0.6938 (mtp) REVERT: A 730 GLU cc_start: 0.7344 (mp0) cc_final: 0.6956 (mp0) REVERT: B 44 THR cc_start: 0.8160 (p) cc_final: 0.7796 (t) REVERT: B 304 GLU cc_start: 0.7626 (tp30) cc_final: 0.7345 (tt0) REVERT: B 333 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: B 483 GLN cc_start: 0.7685 (mp10) cc_final: 0.7405 (mm110) REVERT: B 562 LEU cc_start: 0.7785 (mt) cc_final: 0.7546 (mt) outliers start: 26 outliers final: 11 residues processed: 154 average time/residue: 1.2943 time to fit residues: 214.7790 Evaluate side-chains 137 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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: 0.5980 chunk 69 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3742 r_free = 0.3742 target = 0.151089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126852 restraints weight = 6555.116| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.08 r_work: 0.3378 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10644 Z= 0.256 Angle : 0.646 11.970 14511 Z= 0.315 Chirality : 0.046 0.199 1593 Planarity : 0.005 0.074 1896 Dihedral : 9.913 160.000 1589 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.21 % Allowed : 13.20 % Favored : 82.58 % 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: -0.69 (0.23), residues: 1327 helix: 0.52 (0.23), residues: 512 sheet: -0.41 (0.47), residues: 117 loop : -1.21 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 524 HIS 0.004 0.001 HIS B 55 PHE 0.016 0.002 PHE A 245 TYR 0.022 0.002 TYR A 824 ARG 0.006 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 1.191 Fit side-chains REVERT: A 415 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7908 (mp) REVERT: A 437 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.5928 (m-70) REVERT: A 490 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: A 491 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6285 (mmm-85) REVERT: A 665 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7390 (tp30) REVERT: A 730 GLU cc_start: 0.7502 (mp0) cc_final: 0.7058 (mp0) REVERT: B 44 THR cc_start: 0.8230 (p) cc_final: 0.7850 (t) REVERT: B 319 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6863 (ptt90) REVERT: B 333 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: B 381 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6388 (pt0) REVERT: B 466 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: B 483 GLN cc_start: 0.7650 (mp10) cc_final: 0.7374 (mm110) REVERT: B 562 LEU cc_start: 0.7802 (mt) cc_final: 0.7600 (mt) outliers start: 45 outliers final: 19 residues processed: 155 average time/residue: 1.2613 time to fit residues: 210.8565 Evaluate side-chains 144 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 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 454 SER Chi-restraints excluded: chain B residue 466 GLU 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: 0.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 724 GLN A 734 HIS A 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123136 restraints weight = 6356.765| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.09 r_work: 0.3362 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10644 Z= 0.279 Angle : 0.657 11.498 14511 Z= 0.319 Chirality : 0.046 0.203 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.719 160.532 1589 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.68 % Allowed : 13.86 % Favored : 81.46 % 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: -0.83 (0.23), residues: 1327 helix: 0.39 (0.22), residues: 531 sheet: -0.51 (0.46), residues: 117 loop : -1.32 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 524 HIS 0.004 0.001 HIS B 57 PHE 0.017 0.002 PHE A 245 TYR 0.023 0.002 TYR A 824 ARG 0.008 0.001 ARG B 236 *********************** 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 178 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 1.127 Fit side-chains REVERT: A 415 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 490 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: A 491 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6271 (mmm-85) REVERT: A 547 GLU cc_start: 0.7286 (mp0) cc_final: 0.6980 (mp0) REVERT: A 589 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7913 (tt) REVERT: A 630 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6359 (mtt-85) REVERT: A 646 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7310 (pmm) REVERT: A 665 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7224 (tp30) REVERT: A 730 GLU cc_start: 0.7517 (mp0) cc_final: 0.7002 (mp0) REVERT: B 44 THR cc_start: 0.8302 (p) cc_final: 0.7930 (t) REVERT: B 61 ASP cc_start: 0.8028 (m-30) cc_final: 0.7716 (m-30) REVERT: B 319 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7111 (ptt90) REVERT: B 333 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: B 483 GLN cc_start: 0.7636 (mp10) cc_final: 0.7333 (mm110) REVERT: B 562 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7528 (mt) outliers start: 50 outliers final: 26 residues processed: 164 average time/residue: 1.3301 time to fit residues: 234.5865 Evaluate side-chains 152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 621 ARG 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 646 MET 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 368 ASN 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 553 SER 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: 0.0030 chunk 89 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 281 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.154725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129716 restraints weight = 6117.452| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.06 r_work: 0.3446 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10644 Z= 0.171 Angle : 0.574 11.178 14511 Z= 0.280 Chirality : 0.043 0.174 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.377 155.925 1589 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.31 % Allowed : 15.73 % Favored : 79.96 % 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: 0.70 (0.23), residues: 523 sheet: -0.63 (0.44), residues: 128 loop : -1.19 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 524 HIS 0.002 0.001 HIS A 599 PHE 0.013 0.001 PHE A 245 TYR 0.016 0.001 TYR A 824 ARG 0.009 0.000 ARG B 236 *********************** 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 186 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.168 Fit side-chains REVERT: A 490 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: A 491 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6250 (mmm-85) REVERT: A 547 GLU cc_start: 0.7252 (mp0) cc_final: 0.6970 (mp0) REVERT: A 630 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6403 (mtt-85) REVERT: A 646 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7367 (pmm) REVERT: A 665 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7156 (tp30) REVERT: A 703 MET cc_start: 0.3066 (ttm) cc_final: 0.2569 (ppp) REVERT: A 730 GLU cc_start: 0.7430 (mp0) cc_final: 0.7049 (mp0) REVERT: B 44 THR cc_start: 0.8206 (p) cc_final: 0.7837 (t) REVERT: B 61 ASP cc_start: 0.7971 (m-30) cc_final: 0.7665 (m-30) REVERT: B 432 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6586 (mt) REVERT: B 562 LEU cc_start: 0.7722 (mt) cc_final: 0.7505 (mt) outliers start: 46 outliers final: 21 residues processed: 174 average time/residue: 1.4022 time to fit residues: 261.0417 Evaluate side-chains 141 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 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 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 439 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 644 ILE Chi-restraints excluded: chain A residue 646 MET 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 365 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 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 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN A 724 GLN A 810 ASN B 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126464 restraints weight = 6149.479| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.06 r_work: 0.3403 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10644 Z= 0.227 Angle : 0.608 10.427 14511 Z= 0.296 Chirality : 0.045 0.191 1593 Planarity : 0.005 0.074 1896 Dihedral : 9.362 158.138 1589 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.49 % Allowed : 17.32 % Favored : 78.18 % 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: -0.59 (0.23), residues: 1327 helix: 0.70 (0.23), residues: 523 sheet: -0.56 (0.46), residues: 117 loop : -1.23 (0.24), residues: 687 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 0.013 0.001 PHE A 245 TYR 0.017 0.001 TYR A 824 ARG 0.008 0.001 ARG B 236 *********************** 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 165 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 1.169 Fit side-chains REVERT: A 490 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: A 491 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6239 (mmm-85) REVERT: A 547 GLU cc_start: 0.7257 (mp0) cc_final: 0.6894 (mp0) REVERT: A 589 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7960 (tt) REVERT: A 630 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6421 (mtt-85) REVERT: A 646 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7457 (pmm) REVERT: A 665 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7170 (tp30) REVERT: A 730 GLU cc_start: 0.7491 (mp0) cc_final: 0.7054 (mp0) REVERT: B 44 THR cc_start: 0.8203 (p) cc_final: 0.7828 (t) REVERT: B 61 ASP cc_start: 0.8024 (m-30) cc_final: 0.7676 (m-30) REVERT: B 139 VAL cc_start: 0.7269 (OUTLIER) cc_final: 0.6962 (t) REVERT: B 432 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6625 (mt) REVERT: B 562 LEU cc_start: 0.7594 (mt) cc_final: 0.7387 (mt) outliers start: 48 outliers final: 27 residues processed: 150 average time/residue: 1.2964 time to fit residues: 209.6751 Evaluate side-chains 141 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 646 MET 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 130 LEU Chi-restraints excluded: chain B residue 139 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 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 209 ASN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121442 restraints weight = 6044.289| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 0.99 r_work: 0.3349 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10644 Z= 0.366 Angle : 0.708 12.296 14511 Z= 0.347 Chirality : 0.049 0.245 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.668 163.040 1589 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.15 % Allowed : 17.42 % Favored : 77.43 % 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: -0.90 (0.23), residues: 1327 helix: 0.38 (0.22), residues: 528 sheet: -0.66 (0.45), residues: 119 loop : -1.38 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 524 HIS 0.004 0.001 HIS A 477 PHE 0.014 0.002 PHE A 245 TYR 0.028 0.002 TYR A 824 ARG 0.007 0.001 ARG B 236 *********************** 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 167 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 112 time to evaluate : 1.089 Fit side-chains REVERT: A 415 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8009 (mp) REVERT: A 490 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: A 491 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6297 (mmm-85) REVERT: A 547 GLU cc_start: 0.7313 (mp0) cc_final: 0.6975 (mp0) REVERT: A 589 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 630 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6505 (mtt-85) REVERT: A 646 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7401 (pmm) REVERT: A 665 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7173 (tp30) REVERT: A 730 GLU cc_start: 0.7540 (mp0) cc_final: 0.7021 (mp0) REVERT: B 44 THR cc_start: 0.8185 (p) cc_final: 0.7828 (t) REVERT: B 61 ASP cc_start: 0.8081 (m-30) cc_final: 0.7645 (m-30) REVERT: B 87 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: B 385 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7159 (mt-10) REVERT: B 432 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6517 (mm) REVERT: B 562 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7659 (mt) outliers start: 55 outliers final: 31 residues processed: 155 average time/residue: 1.2632 time to fit residues: 211.0004 Evaluate side-chains 147 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 171 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 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 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 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 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER 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: 0.3980 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.151962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126672 restraints weight = 5962.207| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.05 r_work: 0.3405 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10644 Z= 0.200 Angle : 0.598 11.007 14511 Z= 0.293 Chirality : 0.044 0.190 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.332 157.631 1589 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.49 % Allowed : 18.35 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.23), residues: 1327 helix: 0.66 (0.23), residues: 521 sheet: -0.86 (0.43), residues: 130 loop : -1.28 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 524 HIS 0.004 0.001 HIS A 171 PHE 0.013 0.001 PHE A 245 TYR 0.017 0.001 TYR A 824 ARG 0.009 0.001 ARG B 236 *********************** 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 163 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 1.116 Fit side-chains REVERT: A 490 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: A 491 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6314 (mmm-85) REVERT: A 547 GLU cc_start: 0.7297 (mp0) cc_final: 0.6998 (mp0) REVERT: A 630 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6366 (mtt-85) REVERT: A 646 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7393 (pmm) REVERT: A 665 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7222 (tp30) REVERT: A 730 GLU cc_start: 0.7407 (mp0) cc_final: 0.6970 (mp0) REVERT: B 44 THR cc_start: 0.8149 (p) cc_final: 0.7786 (t) REVERT: B 61 ASP cc_start: 0.8019 (m-30) cc_final: 0.7630 (m-30) REVERT: B 87 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: B 432 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6499 (mt) REVERT: B 562 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7392 (mt) outliers start: 48 outliers final: 28 residues processed: 148 average time/residue: 1.2670 time to fit residues: 202.5278 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 : 1.143 ------------------------------------------------------------------------------- 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 206 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 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 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 646 MET 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 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 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.149506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124025 restraints weight = 6119.173| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.07 r_work: 0.3382 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10644 Z= 0.245 Angle : 0.624 10.891 14511 Z= 0.306 Chirality : 0.045 0.208 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.351 158.667 1589 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.03 % Allowed : 18.45 % Favored : 77.53 % 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: -0.69 (0.23), residues: 1327 helix: 0.64 (0.23), residues: 522 sheet: -0.72 (0.45), residues: 119 loop : -1.30 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 524 HIS 0.003 0.001 HIS B 152 PHE 0.013 0.001 PHE A 245 TYR 0.019 0.001 TYR A 824 ARG 0.009 0.001 ARG B 236 *********************** 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 150 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 1.318 Fit side-chains REVERT: A 415 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 437 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.5457 (m90) REVERT: A 490 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: A 491 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6363 (mmm-85) REVERT: A 547 GLU cc_start: 0.7250 (mp0) cc_final: 0.6960 (mp0) REVERT: A 589 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7911 (tt) REVERT: A 630 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6382 (mtt-85) REVERT: A 646 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7378 (pmm) REVERT: A 665 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7197 (tp30) REVERT: A 713 HIS cc_start: 0.6697 (t-90) cc_final: 0.6316 (t-170) REVERT: A 730 GLU cc_start: 0.7409 (mp0) cc_final: 0.7033 (mp0) REVERT: B 44 THR cc_start: 0.8147 (p) cc_final: 0.7768 (t) REVERT: B 61 ASP cc_start: 0.8103 (m-30) cc_final: 0.7685 (m-30) REVERT: B 87 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: B 432 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6438 (mt) REVERT: B 562 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7335 (mt) outliers start: 43 outliers final: 26 residues processed: 139 average time/residue: 1.2781 time to fit residues: 191.0604 Evaluate side-chains 139 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 9 optimal weight: 0.4980 chunk 111 optimal weight: 0.2980 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128772 restraints weight = 6020.253| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.05 r_work: 0.3443 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10644 Z= 0.178 Angle : 0.581 10.742 14511 Z= 0.284 Chirality : 0.043 0.186 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.161 155.939 1589 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.28 % Allowed : 19.38 % 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: -0.55 (0.23), residues: 1327 helix: 0.79 (0.23), residues: 524 sheet: -0.86 (0.43), residues: 130 loop : -1.20 (0.24), residues: 673 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 0.012 0.001 PHE A 245 TYR 0.014 0.001 TYR B 92 ARG 0.009 0.000 ARG B 236 ********************** 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 155 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.939 Fit side-chains REVERT: A 491 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6314 (mmm-85) REVERT: A 547 GLU cc_start: 0.7207 (mp0) cc_final: 0.6896 (mp0) REVERT: A 630 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6301 (mtt-85) REVERT: A 646 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7355 (pmm) REVERT: A 665 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7219 (tp30) REVERT: A 703 MET cc_start: 0.3694 (ttm) cc_final: 0.2959 (ppp) REVERT: A 713 HIS cc_start: 0.6628 (t-90) cc_final: 0.6201 (t-170) REVERT: A 730 GLU cc_start: 0.7480 (mp0) cc_final: 0.7139 (mp0) REVERT: B 44 THR cc_start: 0.8082 (p) cc_final: 0.7707 (t) REVERT: B 61 ASP cc_start: 0.7991 (m-30) cc_final: 0.7581 (m-30) REVERT: B 110 ILE cc_start: 0.7956 (pt) cc_final: 0.7689 (tt) REVERT: B 385 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7175 (mt-10) REVERT: B 432 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6629 (mt) outliers start: 35 outliers final: 27 residues processed: 145 average time/residue: 1.2888 time to fit residues: 200.9965 Evaluate side-chains 139 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 444 LEU 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 646 MET Chi-restraints excluded: chain A residue 678 THR 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 368 ASN 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: 5.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124597 restraints weight = 6066.167| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.06 r_work: 0.3391 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10644 Z= 0.251 Angle : 0.631 10.846 14511 Z= 0.309 Chirality : 0.046 0.208 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.339 158.736 1589 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.37 % Allowed : 19.29 % 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: -0.63 (0.23), residues: 1327 helix: 0.69 (0.23), residues: 521 sheet: -0.70 (0.45), residues: 119 loop : -1.25 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 524 HIS 0.003 0.001 HIS B 164 PHE 0.013 0.001 PHE A 245 TYR 0.020 0.002 TYR A 824 ARG 0.009 0.001 ARG B 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7144.02 seconds wall clock time: 126 minutes 45.00 seconds (7605.00 seconds total)