Starting phenix.real_space_refine on Tue Feb 3 21:44:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n7e_49093/02_2026/9n7e_49093.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n7e_49093/02_2026/9n7e_49093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n7e_49093/02_2026/9n7e_49093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n7e_49093/02_2026/9n7e_49093.map" model { file = "/net/cci-nas-00/data/ceres_data/9n7e_49093/02_2026/9n7e_49093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n7e_49093/02_2026/9n7e_49093.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 46 5.16 5 C 4469 2.51 5 N 1137 2.21 5 O 1397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7050 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5251 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 31, 'TRANS': 654} Chain breaks: 3 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 9, 'ASN:plan1': 8, 'ASP:plan': 17, 'GLU:plan': 25, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 236 Chain: "B" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1425 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 6, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.32, per 1000 atoms: 0.19 Number of scatterers: 7050 At special positions: 0 Unit cell: (96.1056, 84.0924, 133.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 46 16.00 O 1397 8.00 N 1137 7.00 C 4469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 357 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 452 " distance=2.09 Simple disulfide: pdb=" SG CYS B 411 " - pdb=" SG CYS B 550 " distance=2.05 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 497 " distance=2.04 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=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 801 " - " ASN A 279 " " NAG A 802 " - " ASN A 103 " " NAG A 803 " - " ASN A 215 " " NAG A 804 " - " ASN A 90 " " NAG A 805 " - " ASN A 24 " " NAG B 601 " - " ASN B 372 " " NAG B 602 " - " ASN B 384 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 545 " " NAG E 1 " - " ASN A 431 " " NAG F 1 " - " ASN A 328 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 179.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 806 " - pdb=" NE2 HIS A 377 " 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 59.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 52 removed outlier: 3.535A pdb=" N SER A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.530A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.522A pdb=" N VAL A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.028A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.511A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 193 removed outlier: 4.008A pdb=" N LYS A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.700A pdb=" N GLU A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 218 through 251 removed outlier: 4.221A pdb=" N THR A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 4.082A pdb=" N ASP A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.531A pdb=" N ILE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 4.141A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.669A pdb=" N HIS A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.514A pdb=" N ARG A 392 " --> pdb=" O TYR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.609A pdb=" N SER A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.845A pdb=" N ASN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 483 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.853A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.992A pdb=" N MET A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 removed outlier: 3.706A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.504A pdb=" N GLU A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.703A pdb=" N GLN A 622 " --> pdb=" O TYR A 619 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 623 " --> pdb=" O ALA A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 623' Processing helix chain 'A' and resid 642 through 664 removed outlier: 3.774A pdb=" N MET A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.767A pdb=" N PHE B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 removed outlier: 4.245A pdb=" N LEU B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.436A pdb=" N ALA B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 removed outlier: 5.152A pdb=" N SER B 428 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 431 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 497 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 5.898A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 349 Processing sheet with id=AA4, first strand: chain 'A' and resid 676 through 682 removed outlier: 4.561A pdb=" N VAL A 681 " --> pdb=" O SER A 686 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER A 686 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A 625 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 374 through 378 removed outlier: 8.958A pdb=" N SER B 414 " --> pdb=" O ASN B 547 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASN B 547 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 374 through 378 removed outlier: 6.600A pdb=" N GLN B 541 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU B 415 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER B 539 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 417 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 537 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR B 419 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 535 " --> pdb=" O TYR B 419 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA B 421 " --> pdb=" O GLN B 533 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN B 533 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 396 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 483 through 486 removed outlier: 6.466A pdb=" N THR B 522 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS B 476 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA B 520 " --> pdb=" O CYS B 476 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 510 " --> pdb=" O GLY B 523 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1162 1.32 - 1.46: 2682 1.46 - 1.60: 3155 1.60 - 1.74: 0 1.74 - 1.88: 76 Bond restraints: 7075 Sorted by residual: bond pdb=" C SER B 403 " pdb=" O SER B 403 " ideal model delta sigma weight residual 1.236 1.184 0.052 8.90e-03 1.26e+04 3.38e+01 bond pdb=" C SER B 398 " pdb=" O SER B 398 " ideal model delta sigma weight residual 1.235 1.183 0.052 1.20e-02 6.94e+03 1.86e+01 bond pdb=" CA VAL B 402 " pdb=" C VAL B 402 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.27e-02 6.20e+03 1.53e+01 bond pdb=" C GLN A 525 " pdb=" O GLN A 525 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.48e+01 bond pdb=" C SER B 409 " pdb=" O SER B 409 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.17e-02 7.31e+03 1.37e+01 ... (remaining 7070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 9266 2.16 - 4.33: 345 4.33 - 6.49: 43 6.49 - 8.65: 6 8.65 - 10.81: 1 Bond angle restraints: 9661 Sorted by residual: angle pdb=" N SER B 409 " pdb=" CA SER B 409 " pdb=" C SER B 409 " ideal model delta sigma weight residual 111.28 117.63 -6.35 1.09e+00 8.42e-01 3.40e+01 angle pdb=" N GLY B 410 " pdb=" CA GLY B 410 " pdb=" C GLY B 410 " ideal model delta sigma weight residual 112.51 120.46 -7.95 1.53e+00 4.27e-01 2.70e+01 angle pdb=" CB GLU A 456 " pdb=" CG GLU A 456 " pdb=" CD GLU A 456 " ideal model delta sigma weight residual 112.60 121.05 -8.45 1.70e+00 3.46e-01 2.47e+01 angle pdb=" CA CYS A 133 " pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " ideal model delta sigma weight residual 114.40 125.21 -10.81 2.30e+00 1.89e-01 2.21e+01 angle pdb=" N CYS B 411 " pdb=" CA CYS B 411 " pdb=" C CYS B 411 " ideal model delta sigma weight residual 108.76 100.96 7.80 1.69e+00 3.50e-01 2.13e+01 ... (remaining 9656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 3971 16.80 - 33.61: 284 33.61 - 50.41: 49 50.41 - 67.21: 28 67.21 - 84.02: 8 Dihedral angle restraints: 4340 sinusoidal: 1742 harmonic: 2598 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 30.12 62.88 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA CYS A 133 " pdb=" C CYS A 133 " pdb=" N ASN A 134 " pdb=" CA ASN A 134 " ideal model delta harmonic sigma weight residual -180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CB CYS B 411 " pdb=" SG CYS B 411 " pdb=" SG CYS B 550 " pdb=" CB CYS B 550 " ideal model delta sinusoidal sigma weight residual 93.00 126.92 -33.92 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 4337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 895 0.070 - 0.140: 190 0.140 - 0.210: 15 0.210 - 0.280: 7 0.280 - 0.350: 3 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA SER B 403 " pdb=" N SER B 403 " pdb=" C SER B 403 " pdb=" CB SER B 403 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA LYS B 518 " pdb=" N LYS B 518 " pdb=" C LYS B 518 " pdb=" CB LYS B 518 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA SER B 409 " pdb=" N SER B 409 " pdb=" C SER B 409 " pdb=" CB SER B 409 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1107 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 805 " 0.050 2.00e-02 2.50e+03 4.07e-02 2.07e+01 pdb=" C7 NAG A 805 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG A 805 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG A 805 " -0.065 2.00e-02 2.50e+03 pdb=" O7 NAG A 805 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 410 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLY B 410 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY B 410 " 0.022 2.00e-02 2.50e+03 pdb=" N CYS B 411 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 409 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C SER B 409 " -0.034 2.00e-02 2.50e+03 pdb=" O SER B 409 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 410 " 0.011 2.00e-02 2.50e+03 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 1 2.15 - 2.84: 2311 2.84 - 3.52: 8680 3.52 - 4.21: 17929 4.21 - 4.90: 29474 Nonbonded interactions: 58395 Sorted by model distance: nonbonded pdb=" OE2 GLU A 401 " pdb="ZN ZN A 806 " model vdw 1.459 2.230 nonbonded pdb=" N GLU B 356 " pdb=" O ASN B 382 " model vdw 2.236 3.120 nonbonded pdb=" OH TYR A 182 " pdb=" OD1 ASP A 508 " model vdw 2.269 3.040 nonbonded pdb=" OE2 GLU A 434 " pdb=" NZ LYS A 540 " model vdw 2.278 3.120 nonbonded pdb=" OD2 ASP A 349 " pdb=" O HOH A 901 " model vdw 2.303 3.040 ... (remaining 58390 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.090 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.010 0.443 7099 Z= 0.492 Angle : 0.920 10.813 9720 Z= 0.558 Chirality : 0.060 0.350 1110 Planarity : 0.005 0.042 1210 Dihedral : 13.285 84.017 2641 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.65 % Favored : 97.24 % Rotamer: Outliers : 0.98 % Allowed : 1.14 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.26), residues: 868 helix: -1.50 (0.21), residues: 428 sheet: 0.32 (0.52), residues: 81 loop : -0.51 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 513 TYR 0.019 0.003 TYR A 384 PHE 0.025 0.003 PHE A 511 TRP 0.020 0.003 TRP A 477 HIS 0.007 0.002 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00830 ( 7075) covalent geometry : angle 0.89633 ( 9661) SS BOND : bond 0.02338 ( 7) SS BOND : angle 3.60699 ( 14) hydrogen bonds : bond 0.28893 ( 354) hydrogen bonds : angle 7.76750 ( 1008) metal coordination : bond 0.32200 ( 2) link_BETA1-4 : bond 0.00256 ( 4) link_BETA1-4 : angle 2.08830 ( 12) link_NAG-ASN : bond 0.00557 ( 11) link_NAG-ASN : angle 2.66341 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.151 Fit side-chains REVERT: A 315 MET cc_start: 0.8414 (mtm) cc_final: 0.8199 (mtp) REVERT: A 400 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.7855 (t70) REVERT: A 454 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8666 (tmm) REVERT: A 525 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: B 434 SER cc_start: 0.8297 (t) cc_final: 0.8059 (t) outliers start: 6 outliers final: 1 residues processed: 94 average time/residue: 0.6359 time to fit residues: 62.2141 Evaluate side-chains 78 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 503 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS A 679 ASN B 431 HIS B 484 ASN B 503 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101871 restraints weight = 6798.855| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.52 r_work: 0.2974 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7099 Z= 0.143 Angle : 0.582 7.256 9720 Z= 0.308 Chirality : 0.043 0.171 1110 Planarity : 0.005 0.036 1210 Dihedral : 6.979 58.567 1273 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.81 % Allowed : 7.32 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 868 helix: 0.47 (0.24), residues: 421 sheet: 0.96 (0.53), residues: 80 loop : -0.16 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 650 TYR 0.018 0.002 TYR A 384 PHE 0.016 0.002 PHE A 522 TRP 0.020 0.002 TRP A 162 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7075) covalent geometry : angle 0.56769 ( 9661) SS BOND : bond 0.00588 ( 7) SS BOND : angle 1.62149 ( 14) hydrogen bonds : bond 0.06979 ( 354) hydrogen bonds : angle 4.84708 ( 1008) metal coordination : bond 0.01962 ( 2) link_BETA1-4 : bond 0.00732 ( 4) link_BETA1-4 : angle 1.59335 ( 12) link_NAG-ASN : bond 0.00413 ( 11) link_NAG-ASN : angle 1.86880 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.265 Fit side-chains REVERT: A 37 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 454 MET cc_start: 0.9244 (tmt) cc_final: 0.8862 (tmm) outliers start: 5 outliers final: 0 residues processed: 85 average time/residue: 0.5771 time to fit residues: 51.5961 Evaluate side-chains 74 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116053 restraints weight = 7090.861| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.63 r_work: 0.3252 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7099 Z= 0.117 Angle : 0.519 6.815 9720 Z= 0.271 Chirality : 0.041 0.143 1110 Planarity : 0.004 0.034 1210 Dihedral : 5.558 54.804 1262 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.14 % Allowed : 9.11 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.28), residues: 868 helix: 1.28 (0.25), residues: 429 sheet: 1.27 (0.55), residues: 80 loop : 0.01 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 650 TYR 0.018 0.001 TYR A 384 PHE 0.018 0.001 PHE A 522 TRP 0.019 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7075) covalent geometry : angle 0.50535 ( 9661) SS BOND : bond 0.00405 ( 7) SS BOND : angle 1.27508 ( 14) hydrogen bonds : bond 0.05938 ( 354) hydrogen bonds : angle 4.43682 ( 1008) metal coordination : bond 0.00483 ( 2) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 1.45375 ( 12) link_NAG-ASN : bond 0.00266 ( 11) link_NAG-ASN : angle 1.76760 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.208 Fit side-chains REVERT: A 37 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 454 MET cc_start: 0.9231 (tmt) cc_final: 0.8800 (tmm) outliers start: 7 outliers final: 2 residues processed: 83 average time/residue: 0.5836 time to fit residues: 50.8366 Evaluate side-chains 77 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain B residue 503 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 34 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 0.0270 chunk 83 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.151952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116512 restraints weight = 7211.430| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.67 r_work: 0.3285 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7099 Z= 0.111 Angle : 0.506 6.813 9720 Z= 0.263 Chirality : 0.041 0.147 1110 Planarity : 0.004 0.033 1210 Dihedral : 5.162 53.052 1262 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.63 % Allowed : 9.43 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.28), residues: 868 helix: 1.69 (0.25), residues: 428 sheet: 1.37 (0.57), residues: 81 loop : 0.11 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 650 TYR 0.019 0.001 TYR A 384 PHE 0.016 0.001 PHE A 522 TRP 0.018 0.001 TRP A 162 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7075) covalent geometry : angle 0.49251 ( 9661) SS BOND : bond 0.00487 ( 7) SS BOND : angle 1.41151 ( 14) hydrogen bonds : bond 0.05330 ( 354) hydrogen bonds : angle 4.27656 ( 1008) metal coordination : bond 0.00111 ( 2) link_BETA1-4 : bond 0.00442 ( 4) link_BETA1-4 : angle 1.41732 ( 12) link_NAG-ASN : bond 0.00253 ( 11) link_NAG-ASN : angle 1.69239 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.256 Fit side-chains REVERT: A 37 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 400 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: A 454 MET cc_start: 0.9231 (tmt) cc_final: 0.8809 (tmm) outliers start: 10 outliers final: 3 residues processed: 86 average time/residue: 0.5588 time to fit residues: 50.4256 Evaluate side-chains 82 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 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 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114229 restraints weight = 7195.781| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.66 r_work: 0.3244 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7099 Z= 0.145 Angle : 0.554 7.181 9720 Z= 0.287 Chirality : 0.043 0.159 1110 Planarity : 0.004 0.033 1210 Dihedral : 5.160 51.179 1262 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.79 % Allowed : 11.06 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.28), residues: 868 helix: 1.66 (0.25), residues: 427 sheet: 1.33 (0.58), residues: 81 loop : 0.11 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.021 0.002 TYR A 384 PHE 0.024 0.002 PHE A 522 TRP 0.019 0.002 TRP A 162 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7075) covalent geometry : angle 0.53940 ( 9661) SS BOND : bond 0.00595 ( 7) SS BOND : angle 1.54278 ( 14) hydrogen bonds : bond 0.06335 ( 354) hydrogen bonds : angle 4.27069 ( 1008) metal coordination : bond 0.00049 ( 2) link_BETA1-4 : bond 0.00403 ( 4) link_BETA1-4 : angle 1.57614 ( 12) link_NAG-ASN : bond 0.00246 ( 11) link_NAG-ASN : angle 1.79886 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.264 Fit side-chains REVERT: A 37 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 268 ASP cc_start: 0.8832 (p0) cc_final: 0.8568 (p0) REVERT: A 400 HIS cc_start: 0.9063 (OUTLIER) cc_final: 0.7053 (t-90) REVERT: A 454 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8832 (tmm) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 0.5947 time to fit residues: 51.2156 Evaluate side-chains 84 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115084 restraints weight = 7230.375| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.65 r_work: 0.3258 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7099 Z= 0.123 Angle : 0.529 7.065 9720 Z= 0.274 Chirality : 0.042 0.148 1110 Planarity : 0.004 0.033 1210 Dihedral : 4.929 48.257 1262 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.44 % Allowed : 10.41 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.28), residues: 868 helix: 1.78 (0.25), residues: 429 sheet: 1.35 (0.58), residues: 81 loop : 0.13 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.019 0.001 TYR A 384 PHE 0.019 0.001 PHE A 522 TRP 0.021 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7075) covalent geometry : angle 0.51437 ( 9661) SS BOND : bond 0.00492 ( 7) SS BOND : angle 1.48728 ( 14) hydrogen bonds : bond 0.05727 ( 354) hydrogen bonds : angle 4.21398 ( 1008) metal coordination : bond 0.00036 ( 2) link_BETA1-4 : bond 0.00422 ( 4) link_BETA1-4 : angle 1.53216 ( 12) link_NAG-ASN : bond 0.00233 ( 11) link_NAG-ASN : angle 1.79588 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.246 Fit side-chains REVERT: A 400 HIS cc_start: 0.9003 (OUTLIER) cc_final: 0.6883 (t-90) REVERT: A 454 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8838 (tmm) REVERT: B 363 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7293 (mt) REVERT: B 389 LEU cc_start: 0.7422 (mp) cc_final: 0.7034 (mt) outliers start: 15 outliers final: 5 residues processed: 84 average time/residue: 0.5761 time to fit residues: 50.9382 Evaluate side-chains 84 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114982 restraints weight = 7133.282| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.66 r_work: 0.3257 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7099 Z= 0.131 Angle : 0.546 7.589 9720 Z= 0.282 Chirality : 0.042 0.182 1110 Planarity : 0.004 0.033 1210 Dihedral : 4.887 45.489 1262 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.95 % Allowed : 11.22 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.28), residues: 868 helix: 1.79 (0.25), residues: 429 sheet: 1.36 (0.58), residues: 81 loop : 0.15 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.019 0.002 TYR A 384 PHE 0.021 0.002 PHE A 522 TRP 0.020 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7075) covalent geometry : angle 0.53131 ( 9661) SS BOND : bond 0.00700 ( 7) SS BOND : angle 1.61943 ( 14) hydrogen bonds : bond 0.05881 ( 354) hydrogen bonds : angle 4.22057 ( 1008) metal coordination : bond 0.00057 ( 2) link_BETA1-4 : bond 0.00401 ( 4) link_BETA1-4 : angle 1.54973 ( 12) link_NAG-ASN : bond 0.00227 ( 11) link_NAG-ASN : angle 1.78945 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.264 Fit side-chains REVERT: A 400 HIS cc_start: 0.9024 (OUTLIER) cc_final: 0.6889 (t-90) REVERT: A 454 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8835 (tmm) REVERT: A 525 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8440 (tp40) REVERT: B 389 LEU cc_start: 0.7498 (mp) cc_final: 0.7126 (mt) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.6160 time to fit residues: 53.6579 Evaluate side-chains 85 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 54 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115788 restraints weight = 7232.363| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.66 r_work: 0.3268 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7099 Z= 0.122 Angle : 0.534 7.024 9720 Z= 0.275 Chirality : 0.041 0.165 1110 Planarity : 0.004 0.033 1210 Dihedral : 4.685 42.858 1262 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.11 % Allowed : 11.06 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.28), residues: 868 helix: 1.87 (0.25), residues: 429 sheet: 1.42 (0.59), residues: 81 loop : 0.19 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.018 0.001 TYR A 384 PHE 0.019 0.001 PHE A 522 TRP 0.021 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7075) covalent geometry : angle 0.51875 ( 9661) SS BOND : bond 0.00594 ( 7) SS BOND : angle 1.59337 ( 14) hydrogen bonds : bond 0.05590 ( 354) hydrogen bonds : angle 4.16720 ( 1008) metal coordination : bond 0.00052 ( 2) link_BETA1-4 : bond 0.00400 ( 4) link_BETA1-4 : angle 1.51163 ( 12) link_NAG-ASN : bond 0.00231 ( 11) link_NAG-ASN : angle 1.78830 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.198 Fit side-chains REVERT: A 142 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8699 (mt) REVERT: A 400 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.6875 (t-90) REVERT: A 454 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8831 (tmm) REVERT: B 389 LEU cc_start: 0.7550 (mp) cc_final: 0.7161 (mt) outliers start: 13 outliers final: 4 residues processed: 84 average time/residue: 0.5418 time to fit residues: 47.8173 Evaluate side-chains 82 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 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 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.101685 restraints weight = 6871.127| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.56 r_work: 0.2976 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7099 Z= 0.129 Angle : 0.552 7.116 9720 Z= 0.284 Chirality : 0.042 0.164 1110 Planarity : 0.004 0.033 1210 Dihedral : 4.651 42.768 1262 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.63 % Allowed : 11.71 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.28), residues: 868 helix: 1.87 (0.25), residues: 429 sheet: 1.42 (0.59), residues: 81 loop : 0.17 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.019 0.002 TYR A 384 PHE 0.021 0.002 PHE A 522 TRP 0.020 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7075) covalent geometry : angle 0.53704 ( 9661) SS BOND : bond 0.00572 ( 7) SS BOND : angle 1.80134 ( 14) hydrogen bonds : bond 0.05813 ( 354) hydrogen bonds : angle 4.18152 ( 1008) metal coordination : bond 0.00052 ( 2) link_BETA1-4 : bond 0.00381 ( 4) link_BETA1-4 : angle 1.51795 ( 12) link_NAG-ASN : bond 0.00222 ( 11) link_NAG-ASN : angle 1.80029 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.192 Fit side-chains REVERT: A 142 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8732 (mt) REVERT: A 400 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.6936 (t-90) REVERT: A 454 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8898 (tmm) REVERT: A 525 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8450 (tp40) REVERT: B 389 LEU cc_start: 0.7547 (mp) cc_final: 0.7156 (mt) outliers start: 10 outliers final: 4 residues processed: 80 average time/residue: 0.5944 time to fit residues: 50.0862 Evaluate side-chains 82 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.101558 restraints weight = 6874.109| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.57 r_work: 0.2975 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7099 Z= 0.131 Angle : 0.554 7.116 9720 Z= 0.285 Chirality : 0.042 0.163 1110 Planarity : 0.004 0.033 1210 Dihedral : 4.565 42.253 1262 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.79 % Allowed : 11.54 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.28), residues: 868 helix: 1.87 (0.25), residues: 429 sheet: 1.41 (0.59), residues: 81 loop : 0.17 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.019 0.002 TYR A 384 PHE 0.021 0.001 PHE A 522 TRP 0.020 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7075) covalent geometry : angle 0.53753 ( 9661) SS BOND : bond 0.00561 ( 7) SS BOND : angle 1.89769 ( 14) hydrogen bonds : bond 0.05845 ( 354) hydrogen bonds : angle 4.18599 ( 1008) metal coordination : bond 0.00059 ( 2) link_BETA1-4 : bond 0.00385 ( 4) link_BETA1-4 : angle 1.53034 ( 12) link_NAG-ASN : bond 0.00225 ( 11) link_NAG-ASN : angle 1.82302 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.258 Fit side-chains REVERT: A 142 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8726 (mt) REVERT: A 400 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.6933 (t-90) REVERT: A 454 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8898 (tmm) REVERT: A 525 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8444 (tp40) REVERT: B 362 MET cc_start: 0.6959 (ttt) cc_final: 0.6563 (ttt) REVERT: B 389 LEU cc_start: 0.7553 (mp) cc_final: 0.7165 (mt) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.5781 time to fit residues: 51.0391 Evaluate side-chains 86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102224 restraints weight = 6819.432| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.55 r_work: 0.2982 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7099 Z= 0.124 Angle : 0.553 10.007 9720 Z= 0.282 Chirality : 0.042 0.158 1110 Planarity : 0.004 0.033 1210 Dihedral : 4.457 40.913 1262 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.63 % Allowed : 11.71 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.28), residues: 868 helix: 1.91 (0.25), residues: 429 sheet: 1.44 (0.59), residues: 81 loop : 0.18 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.018 0.001 TYR A 384 PHE 0.019 0.001 PHE A 522 TRP 0.021 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7075) covalent geometry : angle 0.53789 ( 9661) SS BOND : bond 0.00542 ( 7) SS BOND : angle 1.83308 ( 14) hydrogen bonds : bond 0.05643 ( 354) hydrogen bonds : angle 4.16467 ( 1008) metal coordination : bond 0.00049 ( 2) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 1.49064 ( 12) link_NAG-ASN : bond 0.00218 ( 11) link_NAG-ASN : angle 1.79285 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2730.18 seconds wall clock time: 47 minutes 2.14 seconds (2822.14 seconds total)