Starting phenix.real_space_refine on Sat Nov 16 08:58:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/11_2024/7xqw_33402.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/11_2024/7xqw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/11_2024/7xqw_33402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/11_2024/7xqw_33402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/11_2024/7xqw_33402.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xqw_33402/11_2024/7xqw_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-5513/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: 6.31, per 1000 atoms: 0.61 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: 2.29 Conformation dependent library (CDL) restraints added in 1.4 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: 1.02 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: 3.86 Time building geometry restraints manager: 2.57 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.040 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- 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 : 0.998 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: 1.3046 time to fit residues: 262.4108 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 : 1.251 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 : 1.230 Fit side-chains REVERT: A 389 LYS cc_start: 0.7610 (tttm) cc_final: 0.7245 (tttt) REVERT: A 437 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.6195 (m-70) REVERT: A 490 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: B 333 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7366 (tp30) outliers start: 26 outliers final: 11 residues processed: 154 average time/residue: 1.3131 time to fit residues: 217.7557 Evaluate side-chains 133 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 67 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 B 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2195 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= 0.295 Angle : 0.675 12.002 14511 Z= 0.329 Chirality : 0.047 0.208 1593 Planarity : 0.005 0.075 1896 Dihedral : 9.997 161.550 1589 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.40 % Allowed : 13.20 % Favored : 82.40 % 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: -0.77 (0.23), residues: 1327 helix: 0.43 (0.23), residues: 512 sheet: -0.45 (0.47), residues: 117 loop : -1.24 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 524 HIS 0.005 0.001 HIS B 55 PHE 0.017 0.002 PHE A 245 TYR 0.024 0.002 TYR A 824 ARG 0.007 0.001 ARG B 236 *********************** 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: 47 poor density : 125 time to evaluate : 1.000 Fit side-chains REVERT: A 415 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7941 (mp) REVERT: A 437 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6146 (m-70) REVERT: A 490 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: A 491 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6125 (mmm-85) REVERT: A 589 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 630 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6345 (mtt-85) REVERT: A 827 ASP cc_start: 0.5887 (OUTLIER) cc_final: 0.5653 (m-30) REVERT: B 319 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6990 (ptt90) REVERT: B 333 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: B 466 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6255 (mp0) outliers start: 47 outliers final: 20 residues processed: 155 average time/residue: 1.2980 time to fit residues: 216.1962 Evaluate side-chains 137 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 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 119 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.0470 chunk 81 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5282 ------------------------------------------------------------------------------- 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 734 HIS A 810 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2511 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= 0.184 Angle : 0.590 12.097 14511 Z= 0.287 Chirality : 0.044 0.179 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.536 156.569 1589 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.12 % Allowed : 14.98 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1327 helix: 0.72 (0.23), residues: 516 sheet: -0.50 (0.47), residues: 117 loop : -1.23 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 524 HIS 0.002 0.001 HIS A 599 PHE 0.016 0.001 PHE A 245 TYR 0.017 0.001 TYR A 824 ARG 0.007 0.000 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 176 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.128 Fit side-chains REVERT: A 490 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: A 491 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6218 (mmm-85) REVERT: A 646 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7257 (pmm) REVERT: B 333 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7420 (tp30) outliers start: 44 outliers final: 21 residues processed: 163 average time/residue: 1.3032 time to fit residues: 228.3269 Evaluate side-chains 132 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 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 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 B residue 304 GLU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.0010 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 109 optimal weight: 0.0060 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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 810 ASN B 483 GLN B 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10644 Z= 0.185 Angle : 0.589 11.703 14511 Z= 0.285 Chirality : 0.044 0.194 1593 Planarity : 0.005 0.074 1896 Dihedral : 9.333 156.983 1589 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.21 % Allowed : 16.67 % Favored : 79.12 % 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: -0.51 (0.23), residues: 1327 helix: 0.79 (0.23), residues: 517 sheet: -0.54 (0.47), residues: 117 loop : -1.18 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 524 HIS 0.003 0.001 HIS B 152 PHE 0.013 0.001 PHE A 245 TYR 0.023 0.001 TYR A 510 ARG 0.008 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 169 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 1.133 Fit side-chains REVERT: A 490 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: A 491 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6134 (mmm-85) REVERT: A 581 LEU cc_start: 0.7709 (tp) cc_final: 0.7427 (tp) REVERT: B 87 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: B 333 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7433 (tp30) outliers start: 45 outliers final: 27 residues processed: 158 average time/residue: 1.3821 time to fit residues: 234.7875 Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 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 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 304 GLU 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 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 43 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 31 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.0060 chunk 67 optimal weight: 0.7980 overall best weight: 0.4774 ------------------------------------------------------------------------------- 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 810 ASN B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2868 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 : 0.573 11.024 14511 Z= 0.279 Chirality : 0.043 0.212 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.225 156.626 1589 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.49 % Allowed : 17.51 % Favored : 78.00 % 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: -0.47 (0.23), residues: 1327 helix: 0.83 (0.23), residues: 523 sheet: -0.71 (0.45), residues: 128 loop : -1.15 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 524 HIS 0.002 0.001 HIS B 164 PHE 0.012 0.001 PHE A 245 TYR 0.015 0.001 TYR A 824 ARG 0.007 0.000 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 167 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 1.112 Fit side-chains REVERT: A 490 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: A 491 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6235 (mmm-85) REVERT: B 87 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: B 333 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7374 (tp30) outliers start: 48 outliers final: 30 residues processed: 155 average time/residue: 1.2853 time to fit residues: 214.9580 Evaluate side-chains 145 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 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 494 LYS 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 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 304 GLU 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 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 124 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 0.0070 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2924 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= 0.196 Angle : 0.585 10.050 14511 Z= 0.286 Chirality : 0.044 0.188 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.195 157.121 1589 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.40 % Allowed : 17.60 % Favored : 78.00 % 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: -0.48 (0.23), residues: 1327 helix: 0.83 (0.23), residues: 523 sheet: -0.73 (0.45), residues: 128 loop : -1.15 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 524 HIS 0.002 0.001 HIS B 164 PHE 0.012 0.001 PHE A 245 TYR 0.021 0.001 TYR A 510 ARG 0.008 0.000 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 166 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 1.199 Fit side-chains REVERT: A 437 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.5661 (m90) REVERT: A 490 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: A 491 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6151 (mmm-85) REVERT: A 630 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6282 (mtt-85) REVERT: B 87 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: B 139 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.7127 (t) outliers start: 47 outliers final: 30 residues processed: 152 average time/residue: 1.3114 time to fit residues: 214.6562 Evaluate side-chains 140 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 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 494 LYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 304 GLU 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 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2909 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= 0.231 Angle : 0.610 10.231 14511 Z= 0.298 Chirality : 0.045 0.202 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.230 158.662 1589 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.59 % Allowed : 18.07 % 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: -0.54 (0.23), residues: 1327 helix: 0.77 (0.23), residues: 523 sheet: -0.74 (0.45), residues: 128 loop : -1.19 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 524 HIS 0.003 0.001 HIS B 164 PHE 0.012 0.001 PHE A 245 TYR 0.019 0.001 TYR A 824 ARG 0.008 0.000 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 162 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 1.169 Fit side-chains REVERT: A 437 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.5714 (m90) REVERT: A 490 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: A 491 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6133 (mmm-85) REVERT: A 589 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7933 (tt) REVERT: A 630 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6350 (mtt-85) REVERT: B 87 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: B 110 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7809 (mt) outliers start: 49 outliers final: 30 residues processed: 147 average time/residue: 1.3256 time to fit residues: 209.7159 Evaluate side-chains 142 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 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 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2991 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= 0.205 Angle : 0.592 9.904 14511 Z= 0.289 Chirality : 0.044 0.197 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.165 157.887 1589 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.93 % Allowed : 19.01 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.23), residues: 1327 helix: 0.83 (0.23), residues: 523 sheet: -0.76 (0.45), residues: 128 loop : -1.18 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 524 HIS 0.003 0.001 HIS B 55 PHE 0.012 0.001 PHE A 245 TYR 0.023 0.001 TYR A 510 ARG 0.009 0.000 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 152 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 1.190 Fit side-chains REVERT: A 437 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.5662 (m90) REVERT: A 490 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: A 491 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6134 (mmm-85) REVERT: A 589 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7974 (tt) REVERT: A 630 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6308 (mtt-85) REVERT: B 87 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: B 110 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7834 (mt) outliers start: 42 outliers final: 29 residues processed: 139 average time/residue: 1.3932 time to fit residues: 208.4996 Evaluate side-chains 135 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 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 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10644 Z= 0.267 Angle : 0.642 11.166 14511 Z= 0.315 Chirality : 0.046 0.210 1593 Planarity : 0.005 0.074 1896 Dihedral : 9.305 159.711 1589 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.46 % Allowed : 19.76 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1327 helix: 0.64 (0.23), residues: 530 sheet: -0.56 (0.46), residues: 119 loop : -1.26 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 524 HIS 0.004 0.001 HIS B 164 PHE 0.012 0.002 PHE A 245 TYR 0.021 0.002 TYR A 824 ARG 0.008 0.001 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 146 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.087 Fit side-chains REVERT: A 415 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7893 (mp) REVERT: A 437 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.5673 (m90) REVERT: A 490 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: A 491 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6172 (mmm-85) REVERT: A 589 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 630 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6331 (mtt-85) REVERT: B 87 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: B 110 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7820 (mt) outliers start: 37 outliers final: 25 residues processed: 134 average time/residue: 1.3564 time to fit residues: 194.9502 Evaluate side-chains 136 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 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 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 105 optimal weight: 8.9990 chunk 44 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 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 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126391 restraints weight = 5999.303| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.05 r_work: 0.3408 rms_B_bonded: 1.51 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: 0.7421 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= 0.221 Angle : 0.609 10.017 14511 Z= 0.298 Chirality : 0.045 0.200 1593 Planarity : 0.005 0.073 1896 Dihedral : 9.243 158.104 1589 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.37 % Allowed : 20.22 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1327 helix: 0.76 (0.23), residues: 523 sheet: -0.74 (0.44), residues: 130 loop : -1.23 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 524 HIS 0.003 0.001 HIS B 164 PHE 0.012 0.001 PHE A 245 TYR 0.018 0.001 TYR A 824 ARG 0.009 0.000 ARG B 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4037.25 seconds wall clock time: 84 minutes 54.69 seconds (5094.69 seconds total)