Starting phenix.real_space_refine on Fri Jun 13 03:13:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we4_37471/06_2025/8we4_37471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we4_37471/06_2025/8we4_37471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8we4_37471/06_2025/8we4_37471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we4_37471/06_2025/8we4_37471.map" model { file = "/net/cci-nas-00/data/ceres_data/8we4_37471/06_2025/8we4_37471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we4_37471/06_2025/8we4_37471.cif" } resolution = 2.91 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= 0.002 sd= 0.031 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 8038 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 44 5.16 5 C 5285 2.51 5 N 1358 2.21 5 O 1593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8281 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 14, 'TRANS': 180} Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.84, per 1000 atoms: 0.95 Number of scatterers: 8281 At special positions: 0 Unit cell: (80.75, 98.6, 123.25, 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 44 16.00 O 1593 8.00 N 1358 7.00 C 5285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 374 " 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 41.4% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.573A pdb=" N ALA A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 4.034A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.692A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.840A pdb=" N LYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.701A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 removed outlier: 4.427A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.881A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 250 removed outlier: 4.316A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.530A pdb=" N TYR A 255 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.127A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.516A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.533A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.742A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.728A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.900A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.722A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.801A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.515A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.931A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.561A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.852A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.820A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.520A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.335A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.621A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.413A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.002A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.903A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.640A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.823A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.483A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.483A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR L 86 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 888 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: 2.58 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2620 1.34 - 1.46: 2219 1.46 - 1.58: 3601 1.58 - 1.70: 2 1.70 - 1.83: 68 Bond restraints: 8510 Sorted by residual: bond pdb=" C HIS A 34 " pdb=" CA AHIS A 34 " ideal model delta sigma weight residual 1.522 1.578 -0.056 1.40e-02 5.10e+03 1.61e+01 bond pdb=" CE1BHIS A 34 " pdb=" NE2BHIS A 34 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.60e+01 bond pdb=" C HIS A 34 " pdb=" O HIS A 34 " ideal model delta sigma weight residual 1.237 1.289 -0.052 1.31e-02 5.83e+03 1.58e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.358 -0.037 1.00e-02 1.00e+04 1.38e+01 bond pdb=" CE1 HIS A 374 " pdb=" NE2 HIS A 374 " ideal model delta sigma weight residual 1.321 1.358 -0.037 1.00e-02 1.00e+04 1.35e+01 ... (remaining 8505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11231 1.92 - 3.84: 283 3.84 - 5.76: 44 5.76 - 7.69: 10 7.69 - 9.61: 2 Bond angle restraints: 11570 Sorted by residual: angle pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 112.00 102.39 9.61 1.40e+00 5.10e-01 4.71e+01 angle pdb=" O HIS A 34 " pdb=" C HIS A 34 " pdb=" CA AHIS A 34 " ideal model delta sigma weight residual 119.60 126.92 -7.32 1.17e+00 7.31e-01 3.92e+01 angle pdb=" O HIS A 34 " pdb=" C HIS A 34 " pdb=" CA BHIS A 34 " ideal model delta sigma weight residual 119.60 126.18 -6.58 1.17e+00 7.31e-01 3.16e+01 angle pdb=" N ALA A 403 " pdb=" CA ALA A 403 " pdb=" C ALA A 403 " ideal model delta sigma weight residual 113.12 106.88 6.24 1.25e+00 6.40e-01 2.49e+01 angle pdb=" CA PRO A 492 " pdb=" N PRO A 492 " pdb=" CD PRO A 492 " ideal model delta sigma weight residual 112.00 105.02 6.98 1.40e+00 5.10e-01 2.48e+01 ... (remaining 11565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 4636 17.17 - 34.34: 399 34.34 - 51.51: 79 51.51 - 68.68: 17 68.68 - 85.85: 6 Dihedral angle restraints: 5137 sinusoidal: 2165 harmonic: 2972 Sorted by residual: dihedral pdb=" CA CYS B 336 " pdb=" C CYS B 336 " pdb=" N PRO B 337 " pdb=" CA PRO B 337 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PRO B 337 " pdb=" C PRO B 337 " pdb=" N PHE B 338 " pdb=" CA PHE B 338 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE B 358 " pdb=" C ILE B 358 " pdb=" N SER B 359 " pdb=" CA SER B 359 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 866 0.042 - 0.083: 266 0.083 - 0.125: 101 0.125 - 0.167: 8 0.167 - 0.209: 5 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CA ILE A 407 " pdb=" N ILE A 407 " pdb=" C ILE A 407 " pdb=" CB ILE A 407 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL A 404 " pdb=" N VAL A 404 " pdb=" C VAL A 404 " pdb=" CB VAL A 404 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 1243 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 372 " -0.031 2.00e-02 2.50e+03 6.40e-02 4.10e+01 pdb=" C ALA A 372 " 0.111 2.00e-02 2.50e+03 pdb=" O ALA A 372 " -0.042 2.00e-02 2.50e+03 pdb=" N HIS A 373 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " 0.094 5.00e-02 4.00e+02 1.36e-01 2.97e+01 pdb=" N PRO A 469 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 518 " 0.473 9.50e-02 1.11e+02 2.12e-01 2.75e+01 pdb=" NE ARG A 518 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 518 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 518 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 518 " 0.016 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 33 2.48 - 3.08: 5620 3.08 - 3.69: 12029 3.69 - 4.29: 17745 4.29 - 4.90: 29763 Nonbonded interactions: 65190 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 905 " model vdw 1.872 2.230 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.156 3.040 nonbonded pdb=" NH1 ARG A 192 " pdb=" O GLU A 197 " model vdw 2.163 3.120 nonbonded pdb=" OG SER A 331 " pdb=" O ILE A 358 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.205 3.040 ... (remaining 65185 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=0.50 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.770 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.130 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:62.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 : 0.006 0.281 8531 Z= 0.273 Angle : 0.706 9.608 11618 Z= 0.413 Chirality : 0.046 0.209 1246 Planarity : 0.009 0.212 1481 Dihedral : 13.303 85.854 3214 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.95 % Favored : 93.56 % Rotamer: Outliers : 0.45 % Allowed : 1.25 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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 (0.27), residues: 1010 helix: 0.57 (0.30), residues: 364 sheet: 0.62 (0.45), residues: 146 loop : -1.35 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 35 HIS 0.007 0.001 HIS A 378 PHE 0.014 0.001 PHE A 512 TYR 0.022 0.001 TYR A 237 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 7) link_NAG-ASN : angle 2.55445 ( 21) link_BETA1-4 : bond 0.00204 ( 2) link_BETA1-4 : angle 1.00383 ( 6) hydrogen bonds : bond 0.19153 ( 316) hydrogen bonds : angle 7.21100 ( 888) link_BETA1-6 : bond 0.00355 ( 1) link_BETA1-6 : angle 1.27314 ( 3) metal coordination : bond 0.25298 ( 2) SS BOND : bond 0.00311 ( 9) SS BOND : angle 0.85153 ( 18) covalent geometry : bond 0.00446 ( 8510) covalent geometry : angle 0.69792 (11570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.7803 (tttp) cc_final: 0.7499 (mtpp) REVERT: A 75 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6525 (tm-30) REVERT: A 105 SER cc_start: 0.8336 (t) cc_final: 0.8078 (t) REVERT: A 161 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7670 (mtp85) REVERT: A 185 VAL cc_start: 0.8132 (t) cc_final: 0.7918 (p) REVERT: A 557 MET cc_start: 0.8058 (tmm) cc_final: 0.7827 (tmt) REVERT: B 401 VAL cc_start: 0.8406 (p) cc_final: 0.8170 (t) outliers start: 4 outliers final: 2 residues processed: 215 average time/residue: 1.0110 time to fit residues: 233.8155 Evaluate side-chains 184 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 477 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 149 ASN A 175 GLN A 417 HIS A 493 HIS A 580 ASN B 354 ASN B 450 ASN B 487 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122422 restraints weight = 20574.125| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.13 r_work: 0.3473 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8531 Z= 0.145 Angle : 0.607 7.601 11618 Z= 0.313 Chirality : 0.043 0.187 1246 Planarity : 0.006 0.087 1481 Dihedral : 6.581 57.557 1321 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.54 % Favored : 93.26 % Rotamer: Outliers : 0.91 % Allowed : 11.34 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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 (0.27), residues: 1010 helix: 0.59 (0.29), residues: 376 sheet: 0.60 (0.45), residues: 147 loop : -1.50 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 353 HIS 0.008 0.001 HIS A 265 PHE 0.032 0.001 PHE B 371 TYR 0.022 0.001 TYR A 613 ARG 0.006 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 7) link_NAG-ASN : angle 2.80333 ( 21) link_BETA1-4 : bond 0.00513 ( 2) link_BETA1-4 : angle 1.13122 ( 6) hydrogen bonds : bond 0.05310 ( 316) hydrogen bonds : angle 5.03076 ( 888) link_BETA1-6 : bond 0.00580 ( 1) link_BETA1-6 : angle 1.29827 ( 3) metal coordination : bond 0.01242 ( 2) SS BOND : bond 0.00316 ( 9) SS BOND : angle 0.70960 ( 18) covalent geometry : bond 0.00326 ( 8510) covalent geometry : angle 0.59440 (11570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8261 (tttp) cc_final: 0.7982 (mtpp) REVERT: A 75 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 105 SER cc_start: 0.8472 (t) cc_final: 0.8206 (t) REVERT: A 161 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7737 (mtp85) REVERT: A 557 MET cc_start: 0.8219 (tmm) cc_final: 0.8003 (tmt) REVERT: B 401 VAL cc_start: 0.8266 (p) cc_final: 0.8010 (t) outliers start: 8 outliers final: 6 residues processed: 193 average time/residue: 1.0418 time to fit residues: 216.0284 Evaluate side-chains 186 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 180 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 0.0000 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 175 GLN A 580 ASN B 354 ASN B 388 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.141494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.122782 restraints weight = 20677.480| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.15 r_work: 0.3479 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8531 Z= 0.121 Angle : 0.577 7.146 11618 Z= 0.296 Chirality : 0.042 0.180 1246 Planarity : 0.005 0.067 1481 Dihedral : 6.012 53.960 1317 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.24 % Favored : 93.56 % Rotamer: Outliers : 1.36 % Allowed : 14.06 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.52 (0.27), residues: 1010 helix: 0.74 (0.29), residues: 377 sheet: 0.53 (0.44), residues: 147 loop : -1.54 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.007 0.001 HIS A 265 PHE 0.022 0.001 PHE B 371 TYR 0.021 0.001 TYR A 613 ARG 0.006 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 7) link_NAG-ASN : angle 2.65973 ( 21) link_BETA1-4 : bond 0.00396 ( 2) link_BETA1-4 : angle 1.25711 ( 6) hydrogen bonds : bond 0.04419 ( 316) hydrogen bonds : angle 4.61448 ( 888) link_BETA1-6 : bond 0.00408 ( 1) link_BETA1-6 : angle 1.10902 ( 3) metal coordination : bond 0.00407 ( 2) SS BOND : bond 0.00294 ( 9) SS BOND : angle 0.62183 ( 18) covalent geometry : bond 0.00270 ( 8510) covalent geometry : angle 0.56577 (11570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8290 (tttp) cc_final: 0.8008 (mtpp) REVERT: A 75 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 105 SER cc_start: 0.8478 (t) cc_final: 0.8205 (t) REVERT: A 181 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7080 (mm-30) REVERT: A 468 ILE cc_start: 0.7966 (mm) cc_final: 0.7523 (tp) REVERT: A 470 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7859 (mtpp) REVERT: A 557 MET cc_start: 0.8182 (tmm) cc_final: 0.7956 (tmt) REVERT: B 401 VAL cc_start: 0.8287 (p) cc_final: 0.8008 (t) outliers start: 12 outliers final: 6 residues processed: 188 average time/residue: 0.9254 time to fit residues: 187.4793 Evaluate side-chains 186 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 180 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain H residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 0.0270 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 175 GLN A 580 ASN H 39 GLN L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122465 restraints weight = 22332.655| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.30 r_work: 0.3470 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8531 Z= 0.121 Angle : 0.573 7.288 11618 Z= 0.292 Chirality : 0.042 0.167 1246 Planarity : 0.005 0.065 1481 Dihedral : 5.795 53.601 1317 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.54 % Favored : 93.26 % Rotamer: Outliers : 1.47 % Allowed : 15.42 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.49 (0.27), residues: 1010 helix: 0.65 (0.28), residues: 383 sheet: 0.50 (0.44), residues: 147 loop : -1.41 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.006 0.001 HIS A 265 PHE 0.015 0.001 PHE B 371 TYR 0.018 0.001 TYR A 613 ARG 0.007 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 7) link_NAG-ASN : angle 2.60033 ( 21) link_BETA1-4 : bond 0.00434 ( 2) link_BETA1-4 : angle 1.26045 ( 6) hydrogen bonds : bond 0.04176 ( 316) hydrogen bonds : angle 4.45849 ( 888) link_BETA1-6 : bond 0.00508 ( 1) link_BETA1-6 : angle 1.14216 ( 3) metal coordination : bond 0.00277 ( 2) SS BOND : bond 0.00310 ( 9) SS BOND : angle 0.63183 ( 18) covalent geometry : bond 0.00274 ( 8510) covalent geometry : angle 0.56222 (11570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8320 (tttp) cc_final: 0.8029 (mtpp) REVERT: A 75 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 105 SER cc_start: 0.8493 (t) cc_final: 0.8219 (t) REVERT: A 181 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 325 GLN cc_start: 0.8014 (tt0) cc_final: 0.7718 (tt0) REVERT: A 329 GLU cc_start: 0.8159 (pt0) cc_final: 0.7907 (pt0) REVERT: A 468 ILE cc_start: 0.8009 (mm) cc_final: 0.7574 (tp) REVERT: A 470 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7935 (mtpp) REVERT: A 557 MET cc_start: 0.8175 (tmm) cc_final: 0.7948 (tmt) REVERT: A 564 GLU cc_start: 0.8320 (tt0) cc_final: 0.8081 (tt0) REVERT: B 401 VAL cc_start: 0.8288 (p) cc_final: 0.8035 (t) outliers start: 13 outliers final: 9 residues processed: 188 average time/residue: 0.9183 time to fit residues: 186.4624 Evaluate side-chains 188 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain H residue 30 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 175 GLN H 83 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.141362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122319 restraints weight = 21961.678| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.27 r_work: 0.3468 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8531 Z= 0.123 Angle : 0.580 8.798 11618 Z= 0.293 Chirality : 0.042 0.164 1246 Planarity : 0.005 0.062 1481 Dihedral : 5.656 53.751 1317 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.05 % Favored : 93.76 % Rotamer: Outliers : 1.59 % Allowed : 16.10 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.45 (0.27), residues: 1010 helix: 0.80 (0.29), residues: 375 sheet: 0.47 (0.44), residues: 147 loop : -1.46 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.006 0.001 HIS A 265 PHE 0.011 0.001 PHE B 371 TYR 0.015 0.001 TYR A 613 ARG 0.006 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 7) link_NAG-ASN : angle 2.52361 ( 21) link_BETA1-4 : bond 0.00392 ( 2) link_BETA1-4 : angle 1.27226 ( 6) hydrogen bonds : bond 0.04055 ( 316) hydrogen bonds : angle 4.36345 ( 888) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 1.13130 ( 3) metal coordination : bond 0.00307 ( 2) SS BOND : bond 0.00300 ( 9) SS BOND : angle 0.57574 ( 18) covalent geometry : bond 0.00281 ( 8510) covalent geometry : angle 0.56942 (11570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8312 (tttp) cc_final: 0.7995 (mtpp) REVERT: A 75 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7118 (tm-30) REVERT: A 105 SER cc_start: 0.8502 (t) cc_final: 0.8231 (t) REVERT: A 181 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6910 (mm-30) REVERT: A 433 GLU cc_start: 0.7522 (tp30) cc_final: 0.7267 (tp30) REVERT: A 468 ILE cc_start: 0.8065 (mm) cc_final: 0.7614 (tp) REVERT: A 470 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7893 (mtpp) REVERT: A 557 MET cc_start: 0.8168 (tmm) cc_final: 0.7942 (tmt) REVERT: A 580 ASN cc_start: 0.7852 (m-40) cc_final: 0.7594 (m-40) REVERT: B 401 VAL cc_start: 0.8312 (p) cc_final: 0.8083 (t) REVERT: H 94 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.6771 (m-80) outliers start: 14 outliers final: 8 residues processed: 183 average time/residue: 1.0084 time to fit residues: 198.5130 Evaluate side-chains 177 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 175 GLN A 442 GLN B 414 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.141519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124427 restraints weight = 14417.264| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.52 r_work: 0.3527 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8531 Z= 0.120 Angle : 0.590 11.593 11618 Z= 0.295 Chirality : 0.042 0.159 1246 Planarity : 0.005 0.059 1481 Dihedral : 5.644 59.353 1317 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.14 % Favored : 93.66 % Rotamer: Outliers : 1.70 % Allowed : 17.46 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.41 (0.27), residues: 1010 helix: 0.81 (0.29), residues: 373 sheet: 0.45 (0.44), residues: 147 loop : -1.37 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 478 HIS 0.006 0.001 HIS A 265 PHE 0.010 0.001 PHE B 371 TYR 0.012 0.001 TYR A 613 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 7) link_NAG-ASN : angle 2.47413 ( 21) link_BETA1-4 : bond 0.00376 ( 2) link_BETA1-4 : angle 1.23972 ( 6) hydrogen bonds : bond 0.03927 ( 316) hydrogen bonds : angle 4.32925 ( 888) link_BETA1-6 : bond 0.00392 ( 1) link_BETA1-6 : angle 1.14852 ( 3) metal coordination : bond 0.00264 ( 2) SS BOND : bond 0.00305 ( 9) SS BOND : angle 0.59986 ( 18) covalent geometry : bond 0.00274 ( 8510) covalent geometry : angle 0.58019 (11570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8235 (tttp) cc_final: 0.7921 (mtpp) REVERT: A 75 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6987 (tm-30) REVERT: A 105 SER cc_start: 0.8487 (t) cc_final: 0.8204 (t) REVERT: A 181 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6762 (mm-30) REVERT: A 325 GLN cc_start: 0.7865 (tt0) cc_final: 0.7564 (tt0) REVERT: A 347 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8379 (m) REVERT: A 433 GLU cc_start: 0.7418 (tp30) cc_final: 0.7134 (tp30) REVERT: A 468 ILE cc_start: 0.8024 (mm) cc_final: 0.7641 (tp) REVERT: A 470 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7800 (mtpp) REVERT: B 401 VAL cc_start: 0.8278 (p) cc_final: 0.8058 (t) outliers start: 15 outliers final: 12 residues processed: 173 average time/residue: 1.0150 time to fit residues: 188.9017 Evaluate side-chains 177 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 86 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 175 GLN A 524 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126707 restraints weight = 12123.799| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.26 r_work: 0.3571 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8531 Z= 0.105 Angle : 0.579 15.154 11618 Z= 0.288 Chirality : 0.041 0.149 1246 Planarity : 0.005 0.059 1481 Dihedral : 5.281 53.295 1317 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.55 % Favored : 94.25 % Rotamer: Outliers : 1.02 % Allowed : 17.91 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.41 (0.27), residues: 1010 helix: 0.82 (0.29), residues: 376 sheet: 0.47 (0.44), residues: 147 loop : -1.41 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 478 HIS 0.006 0.001 HIS A 265 PHE 0.009 0.001 PHE B 371 TYR 0.012 0.001 TYR A 613 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 7) link_NAG-ASN : angle 2.36387 ( 21) link_BETA1-4 : bond 0.00452 ( 2) link_BETA1-4 : angle 1.21714 ( 6) hydrogen bonds : bond 0.03456 ( 316) hydrogen bonds : angle 4.26084 ( 888) link_BETA1-6 : bond 0.00417 ( 1) link_BETA1-6 : angle 1.21316 ( 3) metal coordination : bond 0.00137 ( 2) SS BOND : bond 0.00280 ( 9) SS BOND : angle 0.59208 ( 18) covalent geometry : bond 0.00231 ( 8510) covalent geometry : angle 0.57011 (11570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8396 (tttp) cc_final: 0.8099 (mtpp) REVERT: A 75 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 105 SER cc_start: 0.8531 (t) cc_final: 0.8260 (t) REVERT: A 181 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 325 GLN cc_start: 0.8131 (tt0) cc_final: 0.7762 (tt0) REVERT: A 329 GLU cc_start: 0.8247 (pt0) cc_final: 0.7966 (pt0) REVERT: A 433 GLU cc_start: 0.7615 (tp30) cc_final: 0.7331 (tp30) REVERT: A 468 ILE cc_start: 0.8081 (mm) cc_final: 0.7656 (tp) REVERT: A 470 LYS cc_start: 0.8418 (mtpp) cc_final: 0.8020 (mtpp) REVERT: A 525 PHE cc_start: 0.8222 (m-80) cc_final: 0.7844 (m-80) REVERT: B 401 VAL cc_start: 0.8318 (p) cc_final: 0.8076 (t) REVERT: B 456 PHE cc_start: 0.8227 (m-80) cc_final: 0.8007 (m-80) outliers start: 9 outliers final: 8 residues processed: 172 average time/residue: 1.0048 time to fit residues: 186.5577 Evaluate side-chains 175 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain H residue 30 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 175 GLN B 450 ASN H 83 ASN L 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.141318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124072 restraints weight = 14978.157| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.57 r_work: 0.3518 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8531 Z= 0.131 Angle : 0.605 16.537 11618 Z= 0.301 Chirality : 0.043 0.153 1246 Planarity : 0.005 0.057 1481 Dihedral : 5.208 53.181 1317 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.95 % Favored : 93.86 % Rotamer: Outliers : 1.47 % Allowed : 18.03 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.42 (0.27), residues: 1010 helix: 0.84 (0.29), residues: 375 sheet: 0.44 (0.44), residues: 147 loop : -1.43 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 478 HIS 0.005 0.001 HIS A 265 PHE 0.012 0.001 PHE A 28 TYR 0.011 0.001 TYR A 613 ARG 0.004 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 7) link_NAG-ASN : angle 2.37337 ( 21) link_BETA1-4 : bond 0.00358 ( 2) link_BETA1-4 : angle 1.21190 ( 6) hydrogen bonds : bond 0.03918 ( 316) hydrogen bonds : angle 4.30122 ( 888) link_BETA1-6 : bond 0.00426 ( 1) link_BETA1-6 : angle 1.11476 ( 3) metal coordination : bond 0.00336 ( 2) SS BOND : bond 0.00316 ( 9) SS BOND : angle 0.64947 ( 18) covalent geometry : bond 0.00304 ( 8510) covalent geometry : angle 0.59656 (11570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8270 (tttp) cc_final: 0.7942 (mtpp) REVERT: A 75 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7001 (tm-30) REVERT: A 105 SER cc_start: 0.8497 (t) cc_final: 0.8211 (t) REVERT: A 171 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: A 181 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6739 (mm-30) REVERT: A 325 GLN cc_start: 0.7869 (tt0) cc_final: 0.7518 (tt0) REVERT: A 329 GLU cc_start: 0.8040 (pt0) cc_final: 0.7709 (pt0) REVERT: A 419 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8293 (mttt) REVERT: A 433 GLU cc_start: 0.7370 (tp30) cc_final: 0.7078 (tp30) REVERT: A 468 ILE cc_start: 0.8019 (mm) cc_final: 0.7579 (tp) REVERT: A 470 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7820 (mtpp) REVERT: B 401 VAL cc_start: 0.8301 (p) cc_final: 0.8096 (t) outliers start: 13 outliers final: 10 residues processed: 174 average time/residue: 0.9480 time to fit residues: 177.6481 Evaluate side-chains 178 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 0.0070 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 175 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.141967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124707 restraints weight = 15097.387| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.58 r_work: 0.3527 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8531 Z= 0.119 Angle : 0.605 16.723 11618 Z= 0.300 Chirality : 0.042 0.155 1246 Planarity : 0.005 0.059 1481 Dihedral : 5.123 53.170 1317 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 1.36 % Allowed : 18.25 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.39 (0.27), residues: 1010 helix: 0.85 (0.29), residues: 375 sheet: 0.51 (0.44), residues: 147 loop : -1.42 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 165 HIS 0.006 0.001 HIS A 265 PHE 0.011 0.001 PHE A 28 TYR 0.011 0.001 TYR A 613 ARG 0.004 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 7) link_NAG-ASN : angle 2.37413 ( 21) link_BETA1-4 : bond 0.00361 ( 2) link_BETA1-4 : angle 1.18570 ( 6) hydrogen bonds : bond 0.03740 ( 316) hydrogen bonds : angle 4.30551 ( 888) link_BETA1-6 : bond 0.00404 ( 1) link_BETA1-6 : angle 1.17000 ( 3) metal coordination : bond 0.00240 ( 2) SS BOND : bond 0.00307 ( 9) SS BOND : angle 0.66773 ( 18) covalent geometry : bond 0.00271 ( 8510) covalent geometry : angle 0.59629 (11570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8276 (tttp) cc_final: 0.7942 (mtpp) REVERT: A 75 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7004 (tm-30) REVERT: A 105 SER cc_start: 0.8505 (t) cc_final: 0.8219 (t) REVERT: A 171 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: A 181 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6677 (mm-30) REVERT: A 325 GLN cc_start: 0.7840 (tt0) cc_final: 0.7478 (tt0) REVERT: A 329 GLU cc_start: 0.8036 (pt0) cc_final: 0.7700 (pt0) REVERT: A 347 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8381 (m) REVERT: A 419 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8279 (mttt) REVERT: A 433 GLU cc_start: 0.7362 (tp30) cc_final: 0.7055 (tp30) REVERT: A 468 ILE cc_start: 0.8035 (mm) cc_final: 0.7643 (tp) REVERT: A 470 LYS cc_start: 0.8284 (mtpp) cc_final: 0.7777 (mtpp) REVERT: A 525 PHE cc_start: 0.7816 (m-80) cc_final: 0.7508 (m-80) REVERT: B 401 VAL cc_start: 0.8290 (p) cc_final: 0.8078 (t) outliers start: 12 outliers final: 9 residues processed: 171 average time/residue: 0.9381 time to fit residues: 172.8123 Evaluate side-chains 175 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 80 optimal weight: 0.4980 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.142219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123195 restraints weight = 22387.170| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.27 r_work: 0.3478 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8531 Z= 0.120 Angle : 0.612 16.466 11618 Z= 0.302 Chirality : 0.042 0.152 1246 Planarity : 0.005 0.058 1481 Dihedral : 5.065 53.247 1317 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 1.13 % Allowed : 18.71 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.42 (0.27), residues: 1010 helix: 0.82 (0.29), residues: 375 sheet: 0.49 (0.44), residues: 147 loop : -1.43 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 165 HIS 0.006 0.001 HIS A 265 PHE 0.010 0.001 PHE A 28 TYR 0.014 0.001 TYR A 237 ARG 0.006 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 7) link_NAG-ASN : angle 2.32828 ( 21) link_BETA1-4 : bond 0.00330 ( 2) link_BETA1-4 : angle 1.16054 ( 6) hydrogen bonds : bond 0.03754 ( 316) hydrogen bonds : angle 4.31723 ( 888) link_BETA1-6 : bond 0.00361 ( 1) link_BETA1-6 : angle 1.14538 ( 3) metal coordination : bond 0.00218 ( 2) SS BOND : bond 0.00305 ( 9) SS BOND : angle 0.68616 ( 18) covalent geometry : bond 0.00277 ( 8510) covalent geometry : angle 0.60351 (11570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8356 (tttp) cc_final: 0.8021 (mtpp) REVERT: A 75 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 105 SER cc_start: 0.8524 (t) cc_final: 0.8239 (t) REVERT: A 181 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6802 (mm-30) REVERT: A 325 GLN cc_start: 0.7956 (tt0) cc_final: 0.7590 (tt0) REVERT: A 329 GLU cc_start: 0.8116 (pt0) cc_final: 0.7780 (pt0) REVERT: A 347 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8392 (m) REVERT: A 419 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8335 (mttt) REVERT: A 433 GLU cc_start: 0.7475 (tp30) cc_final: 0.7160 (tp30) REVERT: A 468 ILE cc_start: 0.8034 (mm) cc_final: 0.7621 (tp) REVERT: A 470 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7843 (mtpp) REVERT: A 525 PHE cc_start: 0.7836 (m-80) cc_final: 0.7472 (m-80) REVERT: B 401 VAL cc_start: 0.8317 (p) cc_final: 0.8102 (t) outliers start: 10 outliers final: 10 residues processed: 171 average time/residue: 0.9422 time to fit residues: 174.1630 Evaluate side-chains 176 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 84 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123751 restraints weight = 17067.289| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.79 r_work: 0.3507 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8531 Z= 0.125 Angle : 0.609 16.837 11618 Z= 0.303 Chirality : 0.042 0.155 1246 Planarity : 0.005 0.058 1481 Dihedral : 5.066 53.446 1317 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 1.36 % Allowed : 18.59 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -0.39 (0.27), residues: 1010 helix: 0.86 (0.29), residues: 375 sheet: 0.48 (0.44), residues: 147 loop : -1.42 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 165 HIS 0.006 0.001 HIS A 265 PHE 0.010 0.001 PHE A 28 TYR 0.011 0.001 TYR A 217 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 7) link_NAG-ASN : angle 2.36598 ( 21) link_BETA1-4 : bond 0.00338 ( 2) link_BETA1-4 : angle 1.16046 ( 6) hydrogen bonds : bond 0.03836 ( 316) hydrogen bonds : angle 4.30733 ( 888) link_BETA1-6 : bond 0.00421 ( 1) link_BETA1-6 : angle 1.14830 ( 3) metal coordination : bond 0.00277 ( 2) SS BOND : bond 0.00318 ( 9) SS BOND : angle 0.69899 ( 18) covalent geometry : bond 0.00288 ( 8510) covalent geometry : angle 0.60081 (11570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6294.68 seconds wall clock time: 108 minutes 36.71 seconds (6516.71 seconds total)