Starting phenix.real_space_refine on Mon Jan 20 02:25:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we4_37471/01_2025/8we4_37471.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we4_37471/01_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_37471/01_2025/8we4_37471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we4_37471/01_2025/8we4_37471.map" model { file = "/net/cci-nas-00/data/ceres_data/8we4_37471/01_2025/8we4_37471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we4_37471/01_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-5571/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: 7.59, per 1000 atoms: 0.92 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: 2.01 Conformation dependent library (CDL) restraints added in 1.5 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: 0.81 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: 2.22 Time building geometry restraints manager: 2.34 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.240 ------------------------------------------------------------------------------- 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 : 0.004 0.129 8510 Z= 0.295 Angle : 0.698 9.608 11570 Z= 0.412 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 *********************** 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 : 0.822 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: 1.0161 time to fit residues: 234.5104 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 : 0.871 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.140732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122203 restraints weight = 20578.182| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.13 r_work: 0.3467 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8510 Z= 0.220 Angle : 0.598 7.526 11570 Z= 0.313 Chirality : 0.044 0.195 1246 Planarity : 0.006 0.087 1481 Dihedral : 6.599 57.617 1321 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.74 % Favored : 93.06 % 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: -0.58 (0.27), residues: 1010 helix: 0.58 (0.29), residues: 376 sheet: 0.58 (0.45), residues: 147 loop : -1.49 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 353 HIS 0.007 0.001 HIS A 265 PHE 0.033 0.001 PHE B 371 TYR 0.022 0.001 TYR A 613 ARG 0.006 0.001 ARG A 177 *********************** 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 : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8262 (tttp) cc_final: 0.7987 (mtpp) REVERT: A 75 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7091 (tm-30) REVERT: A 105 SER cc_start: 0.8475 (t) cc_final: 0.8209 (t) REVERT: A 468 ILE cc_start: 0.7984 (mm) cc_final: 0.7499 (tp) REVERT: A 557 MET cc_start: 0.8222 (tmm) cc_final: 0.8005 (tmt) REVERT: B 401 VAL cc_start: 0.8276 (p) cc_final: 0.8019 (t) outliers start: 8 outliers final: 5 residues processed: 193 average time/residue: 1.0701 time to fit residues: 221.2545 Evaluate side-chains 186 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 181 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 94 optimal weight: 0.0470 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 442 GLN A 580 ASN B 354 ASN B 388 ASN H 39 GLN L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.140269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.121565 restraints weight = 20658.683| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.13 r_work: 0.3457 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8510 Z= 0.212 Angle : 0.579 7.194 11570 Z= 0.301 Chirality : 0.043 0.177 1246 Planarity : 0.005 0.068 1481 Dihedral : 6.065 54.495 1317 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.64 % Favored : 93.16 % Rotamer: Outliers : 1.93 % Allowed : 13.72 % Favored : 84.35 % 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: 0.67 (0.28), residues: 377 sheet: 0.49 (0.44), residues: 147 loop : -1.53 (0.28), residues: 486 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 0.021 0.001 PHE B 371 TYR 0.021 0.001 TYR A 613 ARG 0.006 0.001 ARG A 177 *********************** 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 200 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.960 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: 0.7997 (mtpp) REVERT: A 75 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 105 SER cc_start: 0.8487 (t) cc_final: 0.8220 (t) REVERT: A 181 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7039 (mm-30) REVERT: A 325 GLN cc_start: 0.8130 (tt0) cc_final: 0.7785 (tt0) REVERT: A 329 GLU cc_start: 0.8114 (pt0) cc_final: 0.7910 (pt0) REVERT: A 468 ILE cc_start: 0.8047 (mm) cc_final: 0.7593 (tp) REVERT: A 470 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7886 (mtpp) REVERT: A 534 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8224 (mppt) REVERT: A 557 MET cc_start: 0.8191 (tmm) cc_final: 0.7972 (tmt) REVERT: B 401 VAL cc_start: 0.8322 (p) cc_final: 0.8066 (t) outliers start: 17 outliers final: 11 residues processed: 188 average time/residue: 0.9474 time to fit residues: 191.8866 Evaluate side-chains 191 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 A residue 261 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 L 38 GLN ** 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 = 0.3862 r_free = 0.3862 target = 0.140416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121281 restraints weight = 22320.289| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.29 r_work: 0.3451 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8510 Z= 0.198 Angle : 0.580 7.577 11570 Z= 0.298 Chirality : 0.043 0.172 1246 Planarity : 0.005 0.066 1481 Dihedral : 5.814 53.935 1317 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.64 % Favored : 93.16 % Rotamer: Outliers : 1.81 % Allowed : 14.63 % Favored : 83.56 % 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: -0.54 (0.27), residues: 1010 helix: 0.72 (0.29), residues: 375 sheet: 0.43 (0.44), residues: 147 loop : -1.51 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 353 HIS 0.006 0.001 HIS A 265 PHE 0.015 0.001 PHE B 371 TYR 0.022 0.001 TYR A 613 ARG 0.008 0.000 ARG A 192 *********************** 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 202 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8322 (tttp) cc_final: 0.8006 (mtpp) REVERT: A 75 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 105 SER cc_start: 0.8504 (t) cc_final: 0.8233 (t) REVERT: A 181 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 433 GLU cc_start: 0.7555 (tp30) cc_final: 0.7320 (tp30) REVERT: A 468 ILE cc_start: 0.8073 (mm) cc_final: 0.7612 (tp) REVERT: A 470 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7992 (mtpp) REVERT: A 557 MET cc_start: 0.8195 (tmm) cc_final: 0.7980 (tmt) REVERT: A 564 GLU cc_start: 0.8321 (tt0) cc_final: 0.8066 (tt0) REVERT: B 401 VAL cc_start: 0.8322 (p) cc_final: 0.8082 (t) outliers start: 16 outliers final: 12 residues processed: 188 average time/residue: 0.9937 time to fit residues: 201.2275 Evaluate side-chains 193 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 388 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 = 0.3847 r_free = 0.3847 target = 0.139311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120235 restraints weight = 21976.285| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.25 r_work: 0.3439 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8510 Z= 0.238 Angle : 0.593 9.003 11570 Z= 0.304 Chirality : 0.043 0.174 1246 Planarity : 0.005 0.063 1481 Dihedral : 5.574 53.825 1317 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.64 % Favored : 93.16 % Rotamer: Outliers : 1.70 % Allowed : 16.21 % Favored : 82.09 % 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: -0.60 (0.27), residues: 1010 helix: 0.64 (0.28), residues: 379 sheet: 0.37 (0.44), residues: 147 loop : -1.52 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 353 HIS 0.007 0.001 HIS A 265 PHE 0.012 0.001 PHE A 28 TYR 0.019 0.001 TYR A 613 ARG 0.008 0.001 ARG A 192 *********************** 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 198 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8281 (tttp) cc_final: 0.7993 (mtpp) REVERT: A 75 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 105 SER cc_start: 0.8525 (t) cc_final: 0.8250 (t) REVERT: A 181 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6948 (mm-30) REVERT: A 325 GLN cc_start: 0.8008 (tt0) cc_final: 0.7659 (tt0) REVERT: A 347 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8385 (m) REVERT: A 433 GLU cc_start: 0.7594 (tp30) cc_final: 0.7289 (tp30) REVERT: A 468 ILE cc_start: 0.8137 (mm) cc_final: 0.7681 (tp) REVERT: A 470 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7951 (mtpp) REVERT: A 557 MET cc_start: 0.8166 (tmm) cc_final: 0.7962 (tmt) REVERT: B 401 VAL cc_start: 0.8394 (p) cc_final: 0.8189 (t) outliers start: 15 outliers final: 11 residues processed: 189 average time/residue: 1.0516 time to fit residues: 214.0612 Evaluate side-chains 190 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 30 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 414 GLN ** 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 = 0.3851 r_free = 0.3851 target = 0.139565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.122558 restraints weight = 14433.027| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.51 r_work: 0.3497 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8510 Z= 0.217 Angle : 0.601 10.763 11570 Z= 0.306 Chirality : 0.043 0.169 1246 Planarity : 0.005 0.061 1481 Dihedral : 5.338 53.567 1317 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.05 % Favored : 93.76 % Rotamer: Outliers : 2.04 % Allowed : 17.12 % 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: -0.58 (0.27), residues: 1010 helix: 0.64 (0.29), residues: 377 sheet: 0.30 (0.44), residues: 147 loop : -1.45 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 163 HIS 0.007 0.001 HIS A 265 PHE 0.011 0.001 PHE A 428 TYR 0.020 0.001 TYR A 613 ARG 0.004 0.000 ARG A 192 *********************** 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 195 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8253 (tttp) cc_final: 0.7966 (mtpp) REVERT: A 75 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7001 (tm-30) REVERT: A 105 SER cc_start: 0.8502 (t) cc_final: 0.8224 (t) REVERT: A 181 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6787 (mm-30) REVERT: A 325 GLN cc_start: 0.7881 (tt0) cc_final: 0.7599 (tt0) REVERT: A 329 GLU cc_start: 0.8082 (pt0) cc_final: 0.7807 (pt0) REVERT: A 347 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8380 (m) REVERT: A 433 GLU cc_start: 0.7432 (tp30) cc_final: 0.7145 (tp30) REVERT: A 468 ILE cc_start: 0.8093 (mm) cc_final: 0.7671 (tp) REVERT: A 470 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7880 (mtpp) REVERT: B 401 VAL cc_start: 0.8317 (p) cc_final: 0.8106 (t) outliers start: 18 outliers final: 11 residues processed: 184 average time/residue: 1.0155 time to fit residues: 201.0004 Evaluate side-chains 184 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 THR 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: 1.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122911 restraints weight = 12139.983| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.23 r_work: 0.3512 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8510 Z= 0.238 Angle : 0.606 13.250 11570 Z= 0.308 Chirality : 0.043 0.169 1246 Planarity : 0.005 0.062 1481 Dihedral : 5.283 53.606 1317 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.54 % Favored : 93.26 % Rotamer: Outliers : 1.81 % Allowed : 17.23 % Favored : 80.95 % 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: -0.67 (0.27), residues: 1010 helix: 0.56 (0.28), residues: 379 sheet: 0.27 (0.44), residues: 147 loop : -1.51 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 163 HIS 0.007 0.001 HIS A 265 PHE 0.012 0.001 PHE A 428 TYR 0.016 0.001 TYR A 613 ARG 0.005 0.000 ARG A 192 *********************** 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 202 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8355 (tttp) cc_final: 0.8068 (mtpp) REVERT: A 75 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7230 (tm-30) REVERT: A 105 SER cc_start: 0.8572 (t) cc_final: 0.8302 (t) REVERT: A 181 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7040 (mm-30) REVERT: A 325 GLN cc_start: 0.8127 (tt0) cc_final: 0.7814 (tt0) REVERT: A 329 GLU cc_start: 0.8296 (pt0) cc_final: 0.8031 (pt0) REVERT: A 347 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8409 (m) REVERT: A 433 GLU cc_start: 0.7755 (tp30) cc_final: 0.7446 (tp30) REVERT: A 468 ILE cc_start: 0.8233 (mm) cc_final: 0.7755 (tp) REVERT: A 470 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8026 (mtpp) REVERT: B 401 VAL cc_start: 0.8412 (p) cc_final: 0.8206 (t) outliers start: 16 outliers final: 10 residues processed: 192 average time/residue: 0.9619 time to fit residues: 198.9619 Evaluate side-chains 195 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 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 50 THR Chi-restraints excluded: chain H residue 82 MET 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: 0.6980 chunk 96 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 47 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3862 r_free = 0.3862 target = 0.140225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123145 restraints weight = 14974.607| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.55 r_work: 0.3504 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 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 = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8510 Z= 0.180 Angle : 0.598 15.989 11570 Z= 0.301 Chirality : 0.043 0.161 1246 Planarity : 0.005 0.061 1481 Dihedral : 5.206 53.372 1317 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.85 % Favored : 93.95 % Rotamer: Outliers : 2.38 % Allowed : 17.35 % Favored : 80.27 % 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: -0.62 (0.27), residues: 1010 helix: 0.62 (0.29), residues: 377 sheet: 0.29 (0.44), residues: 147 loop : -1.48 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 163 HIS 0.007 0.001 HIS A 265 PHE 0.010 0.001 PHE A 428 TYR 0.015 0.001 TYR A 613 ARG 0.006 0.000 ARG A 192 *********************** 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 205 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8270 (tttp) cc_final: 0.7941 (mtpp) REVERT: A 75 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7000 (tm-30) REVERT: A 105 SER cc_start: 0.8504 (t) cc_final: 0.8229 (t) REVERT: A 131 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7441 (ttmm) REVERT: A 171 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: A 181 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6756 (mm-30) REVERT: A 325 GLN cc_start: 0.7870 (tt0) cc_final: 0.7542 (tt0) REVERT: A 329 GLU cc_start: 0.8055 (pt0) cc_final: 0.7711 (pt0) REVERT: A 347 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8378 (m) REVERT: A 433 GLU cc_start: 0.7450 (tp30) cc_final: 0.7130 (tp30) REVERT: A 468 ILE cc_start: 0.8091 (mm) cc_final: 0.7664 (tp) REVERT: A 470 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7887 (mtpp) REVERT: A 525 PHE cc_start: 0.8100 (m-80) cc_final: 0.7733 (m-80) REVERT: B 401 VAL cc_start: 0.8305 (p) cc_final: 0.8084 (t) REVERT: B 489 TYR cc_start: 0.8176 (m-80) cc_final: 0.7545 (m-80) outliers start: 21 outliers final: 13 residues processed: 189 average time/residue: 0.9918 time to fit residues: 201.7024 Evaluate side-chains 199 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 249 MET 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 446 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 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: 0.0370 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 68 optimal weight: 0.0060 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3074 ------------------------------------------------------------------------------- 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 345 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.141699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124564 restraints weight = 15100.064| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.55 r_work: 0.3527 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 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 = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8510 Z= 0.152 Angle : 0.583 16.126 11570 Z= 0.292 Chirality : 0.042 0.147 1246 Planarity : 0.005 0.060 1481 Dihedral : 5.091 53.193 1317 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 1.93 % Allowed : 18.48 % Favored : 79.59 % 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: -0.53 (0.27), residues: 1010 helix: 0.72 (0.29), residues: 377 sheet: 0.34 (0.44), residues: 147 loop : -1.47 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 163 HIS 0.006 0.001 HIS A 265 PHE 0.009 0.001 PHE A 428 TYR 0.014 0.001 TYR A 613 ARG 0.005 0.000 ARG A 115 *********************** 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 192 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8280 (tttp) cc_final: 0.7969 (mtpp) REVERT: A 75 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7037 (tm-30) REVERT: A 105 SER cc_start: 0.8494 (t) cc_final: 0.8216 (t) REVERT: A 171 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: A 181 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6714 (mm-30) REVERT: A 325 GLN cc_start: 0.7865 (tt0) cc_final: 0.7502 (tt0) REVERT: A 329 GLU cc_start: 0.8010 (pt0) cc_final: 0.7654 (pt0) REVERT: A 347 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8369 (m) REVERT: A 419 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8420 (mttt) REVERT: A 433 GLU cc_start: 0.7342 (tp30) cc_final: 0.7014 (tp30) REVERT: A 468 ILE cc_start: 0.8032 (mm) cc_final: 0.7681 (tp) REVERT: A 470 LYS cc_start: 0.8316 (mtpp) cc_final: 0.7896 (mtpp) REVERT: A 525 PHE cc_start: 0.7991 (m-80) cc_final: 0.7564 (m-80) REVERT: B 401 VAL cc_start: 0.8255 (p) cc_final: 0.8005 (t) REVERT: B 442 ASP cc_start: 0.7818 (m-30) cc_final: 0.7603 (m-30) REVERT: B 489 TYR cc_start: 0.8141 (m-80) cc_final: 0.7566 (m-80) outliers start: 17 outliers final: 11 residues processed: 182 average time/residue: 1.0897 time to fit residues: 213.8366 Evaluate side-chains 183 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 249 MET 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 B residue 490 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 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: 0.9990 chunk 94 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 B 450 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 = 0.3845 r_free = 0.3845 target = 0.139067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120220 restraints weight = 22402.461| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.24 r_work: 0.3429 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8510 Z= 0.248 Angle : 0.634 17.520 11570 Z= 0.318 Chirality : 0.044 0.161 1246 Planarity : 0.005 0.059 1481 Dihedral : 5.212 53.920 1317 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.74 % Favored : 93.06 % Rotamer: Outliers : 1.81 % Allowed : 18.71 % Favored : 79.48 % 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: -0.58 (0.27), residues: 1010 helix: 0.64 (0.29), residues: 377 sheet: 0.30 (0.44), residues: 147 loop : -1.46 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 163 HIS 0.006 0.001 HIS A 265 PHE 0.012 0.001 PHE A 285 TYR 0.014 0.001 TYR A 613 ARG 0.005 0.001 ARG A 460 ********************** 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 195 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8319 (tttp) cc_final: 0.8011 (mtpp) REVERT: A 75 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 105 SER cc_start: 0.8510 (t) cc_final: 0.8232 (t) REVERT: A 167 SER cc_start: 0.8229 (t) cc_final: 0.7187 (t) REVERT: A 171 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: A 181 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 325 GLN cc_start: 0.8024 (tt0) cc_final: 0.7649 (tt0) REVERT: A 329 GLU cc_start: 0.8158 (pt0) cc_final: 0.7843 (pt0) REVERT: A 347 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8368 (m) REVERT: A 419 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8519 (mttt) REVERT: A 433 GLU cc_start: 0.7548 (tp30) cc_final: 0.7217 (tp30) REVERT: A 468 ILE cc_start: 0.8171 (mm) cc_final: 0.7723 (tp) REVERT: A 470 LYS cc_start: 0.8379 (mtpp) cc_final: 0.7909 (mtpp) REVERT: A 525 PHE cc_start: 0.8077 (m-80) cc_final: 0.7654 (m-80) REVERT: B 396 TYR cc_start: 0.8259 (m-80) cc_final: 0.8031 (m-80) outliers start: 16 outliers final: 11 residues processed: 185 average time/residue: 1.0438 time to fit residues: 207.3350 Evaluate side-chains 194 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 GLU 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 446 SER Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 490 SER 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: 0.8980 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 83 optimal weight: 0.0980 chunk 37 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122959 restraints weight = 17070.603| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.74 r_work: 0.3501 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8510 Z= 0.166 Angle : 0.606 16.476 11570 Z= 0.303 Chirality : 0.042 0.152 1246 Planarity : 0.005 0.060 1481 Dihedral : 5.135 53.780 1317 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.24 % Favored : 93.56 % Rotamer: Outliers : 1.25 % Allowed : 19.16 % Favored : 79.59 % 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: -0.55 (0.27), residues: 1010 helix: 0.72 (0.29), residues: 377 sheet: 0.24 (0.42), residues: 153 loop : -1.47 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 163 HIS 0.007 0.001 HIS A 265 PHE 0.009 0.001 PHE A 428 TYR 0.015 0.001 TYR A 613 ARG 0.007 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6103.85 seconds wall clock time: 110 minutes 19.83 seconds (6619.83 seconds total)