Starting phenix.real_space_refine on Wed May 14 11:24:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhf_38349/05_2025/8xhf_38349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhf_38349/05_2025/8xhf_38349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhf_38349/05_2025/8xhf_38349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhf_38349/05_2025/8xhf_38349.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhf_38349/05_2025/8xhf_38349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhf_38349/05_2025/8xhf_38349.cif" } resolution = 2.39 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 7356 2.51 5 N 2001 2.21 5 O 2304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11736 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3870 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 19, 'TRANS': 468} Chain breaks: 1 Chain: "A" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3870 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 19, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3870 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 19, 'TRANS': 468} Chain breaks: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.75, per 1000 atoms: 0.66 Number of scatterers: 11736 At special positions: 0 Unit cell: (87.55, 87.55, 150.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2304 8.00 N 2001 7.00 C 7356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 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 NAG-ASN " NAG A 601 " - " ASN A 169 " " NAG A 602 " - " ASN A 484 " " NAG A 603 " - " ASN A 28 " " NAG B 601 " - " ASN B 169 " " NAG B 602 " - " ASN B 28 " " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 28 " " NAG C 603 " - " ASN C 484 " " NAG C 604 " - " ASN C 290 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2682 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 33 sheets defined 28.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.787A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 368 through 387 Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.702A pdb=" N GLU C 435 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.901A pdb=" N ASP A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.801A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.645A pdb=" N GLU A 341 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 388 Processing helix chain 'A' and resid 404 through 457 removed outlier: 3.780A pdb=" N ASP A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.554A pdb=" N LEU A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.915A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 388 removed outlier: 3.619A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 457 removed outlier: 3.623A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 445 " --> pdb=" O HIS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 488 through 500 removed outlier: 4.515A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 363 through 364 removed outlier: 3.587A pdb=" N GLY C 11 " --> pdb=" O GLY C 353 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.366A pdb=" N LEU C 46 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.641A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.344A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS C 115 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG C 263 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 113 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 100 removed outlier: 7.909A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.921A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.316A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.730A pdb=" N GLY A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 356 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 11 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AB6, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AB7, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.061A pdb=" N LYS A 48 " --> pdb=" O THR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.603A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.470A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.899A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AC3, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.885A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AC6, first strand: chain 'B' and resid 362 through 364 removed outlier: 3.565A pdb=" N GLY B 11 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 7 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AC9, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AD1, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.623A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.654A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.654A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.519A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 146 " --> pdb=" O CYS B 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'B' and resid 287 through 289 removed outlier: 4.588A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 3.27 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: 3866 1.34 - 1.46: 2822 1.46 - 1.58: 5192 1.58 - 1.70: 0 1.70 - 1.83: 114 Bond restraints: 11994 Sorted by residual: bond pdb=" C TYR B 489 " pdb=" N PRO B 490 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.46e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C1 NAG C 604 " pdb=" O5 NAG C 604 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CB LYS B 473 " pdb=" CG LYS B 473 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 ... (remaining 11989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15879 1.55 - 3.10: 308 3.10 - 4.64: 31 4.64 - 6.19: 7 6.19 - 7.74: 2 Bond angle restraints: 16227 Sorted by residual: angle pdb=" C ARG C 457 " pdb=" CA ARG C 457 " pdb=" CB ARG C 457 " ideal model delta sigma weight residual 116.63 110.29 6.34 1.16e+00 7.43e-01 2.99e+01 angle pdb=" CB LYS B 473 " pdb=" CG LYS B 473 " pdb=" CD LYS B 473 " ideal model delta sigma weight residual 111.30 119.04 -7.74 2.30e+00 1.89e-01 1.13e+01 angle pdb=" CA ARG C 457 " pdb=" C ARG C 457 " pdb=" N ASP C 458 " ideal model delta sigma weight residual 119.63 117.05 2.58 8.10e-01 1.52e+00 1.02e+01 angle pdb=" N ARG C 457 " pdb=" CA ARG C 457 " pdb=" C ARG C 457 " ideal model delta sigma weight residual 108.08 112.66 -4.58 1.69e+00 3.50e-01 7.35e+00 angle pdb=" CA CYS B 278 " pdb=" CB CYS B 278 " pdb=" SG CYS B 278 " ideal model delta sigma weight residual 114.40 120.32 -5.92 2.30e+00 1.89e-01 6.63e+00 ... (remaining 16222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 6066 18.22 - 36.43: 879 36.43 - 54.65: 301 54.65 - 72.86: 51 72.86 - 91.08: 20 Dihedral angle restraints: 7317 sinusoidal: 3120 harmonic: 4197 Sorted by residual: dihedral pdb=" CB CYS B 47 " pdb=" SG CYS B 47 " pdb=" SG CYS B 278 " pdb=" CB CYS B 278 " ideal model delta sinusoidal sigma weight residual -86.00 -12.07 -73.93 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 72 " pdb=" CB CYS A 72 " ideal model delta sinusoidal sigma weight residual 93.00 132.51 -39.51 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N CYS B 47 " pdb=" CA CYS B 47 " ideal model delta harmonic sigma weight residual -180.00 -159.90 -20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1446 0.052 - 0.105: 256 0.105 - 0.157: 67 0.157 - 0.210: 0 0.210 - 0.262: 1 Chirality restraints: 1770 Sorted by residual: chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 28 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO B 307 " pdb=" N PRO B 307 " pdb=" C PRO B 307 " pdb=" CB PRO B 307 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 28 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1767 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 339 " 0.011 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE C 339 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 339 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 339 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 339 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 339 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 339 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 18 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C THR C 18 " 0.026 2.00e-02 2.50e+03 pdb=" O THR C 18 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU C 19 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 415 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" CD GLU B 415 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU B 415 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU B 415 " 0.008 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 976 2.74 - 3.28: 10299 3.28 - 3.82: 18841 3.82 - 4.36: 22641 4.36 - 4.90: 40060 Nonbonded interactions: 92817 Sorted by model distance: nonbonded pdb=" O SER B 112 " pdb=" OG SER B 112 " model vdw 2.199 3.040 nonbonded pdb=" O SER B 142 " pdb=" OG SER B 142 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN C 15 " pdb=" OG SER C 17 " model vdw 2.247 3.040 nonbonded pdb=" O SER C 112 " pdb=" OG SER C 112 " model vdw 2.275 3.040 nonbonded pdb=" O SER A 159 " pdb=" OG SER A 159 " model vdw 2.316 3.040 ... (remaining 92812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 500 or resid 601 through 602)) selection = chain 'B' selection = (chain 'C' and (resid 6 through 500 or resid 601 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.670 Find NCS groups from input model: 0.580 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:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 0.040 12021 Z= 0.172 Angle : 0.534 7.738 16290 Z= 0.281 Chirality : 0.043 0.262 1770 Planarity : 0.004 0.043 2097 Dihedral : 19.113 91.078 4581 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 4.42 % Allowed : 29.53 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.22), residues: 1452 helix: 2.16 (0.27), residues: 375 sheet: 0.89 (0.31), residues: 294 loop : -1.59 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 422 HIS 0.012 0.001 HIS C 356 PHE 0.030 0.002 PHE C 339 TYR 0.018 0.001 TYR A 12 ARG 0.010 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 9) link_NAG-ASN : angle 1.79231 ( 27) hydrogen bonds : bond 0.17671 ( 462) hydrogen bonds : angle 6.96667 ( 1356) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.26767 ( 36) covalent geometry : bond 0.00397 (11994) covalent geometry : angle 0.52641 (16227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 301 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 ASP cc_start: 0.7725 (t0) cc_final: 0.7439 (t0) outliers start: 57 outliers final: 50 residues processed: 354 average time/residue: 1.3364 time to fit residues: 506.9981 Evaluate side-chains 347 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 297 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 492 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.5980 chunk 109 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.0010 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS C 499 ASN A 380 ASN A 392 GLN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN B 472 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114290 restraints weight = 15480.169| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.69 r_work: 0.3504 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12021 Z= 0.115 Angle : 0.504 9.580 16290 Z= 0.270 Chirality : 0.041 0.244 1770 Planarity : 0.004 0.031 2097 Dihedral : 8.062 64.854 1845 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.74 % Allowed : 25.66 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.22), residues: 1452 helix: 2.50 (0.27), residues: 378 sheet: 0.68 (0.31), residues: 312 loop : -1.30 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.011 0.001 HIS B 472 PHE 0.017 0.001 PHE A 295 TYR 0.012 0.001 TYR A 12 ARG 0.006 0.000 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 9) link_NAG-ASN : angle 1.78373 ( 27) hydrogen bonds : bond 0.05155 ( 462) hydrogen bonds : angle 5.09787 ( 1356) SS BOND : bond 0.00550 ( 18) SS BOND : angle 1.37181 ( 36) covalent geometry : bond 0.00252 (11994) covalent geometry : angle 0.49552 (16227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 320 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8477 (p) cc_final: 0.8249 (t) REVERT: C 491 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7616 (tttm) REVERT: A 67 LEU cc_start: 0.8767 (mt) cc_final: 0.8489 (mt) REVERT: A 456 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 479 MET cc_start: 0.7974 (tpp) cc_final: 0.7486 (mmp) REVERT: B 491 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7367 (mtpt) outliers start: 74 outliers final: 35 residues processed: 364 average time/residue: 1.3062 time to fit residues: 510.7588 Evaluate side-chains 351 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 143 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS C 499 ASN A 380 ASN B 186 ASN B 224 ASN B 296 HIS B 459 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.127021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114172 restraints weight = 15590.823| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.70 r_work: 0.3512 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12021 Z= 0.116 Angle : 0.495 10.387 16290 Z= 0.264 Chirality : 0.042 0.253 1770 Planarity : 0.004 0.034 2097 Dihedral : 6.932 84.507 1793 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.81 % Allowed : 26.28 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.23), residues: 1452 helix: 2.66 (0.27), residues: 378 sheet: 0.56 (0.31), residues: 318 loop : -1.19 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 422 HIS 0.010 0.001 HIS C 356 PHE 0.020 0.001 PHE C 339 TYR 0.014 0.001 TYR A 12 ARG 0.007 0.001 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 9) link_NAG-ASN : angle 1.89982 ( 27) hydrogen bonds : bond 0.04952 ( 462) hydrogen bonds : angle 4.85994 ( 1356) SS BOND : bond 0.00551 ( 18) SS BOND : angle 1.22145 ( 36) covalent geometry : bond 0.00260 (11994) covalent geometry : angle 0.48675 (16227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 319 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8438 (p) cc_final: 0.8219 (t) REVERT: C 491 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7593 (tttm) REVERT: A 456 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 458 ASP cc_start: 0.7976 (t0) cc_final: 0.7663 (t0) REVERT: A 479 MET cc_start: 0.8007 (tpp) cc_final: 0.7660 (mmp) REVERT: B 436 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7383 (mpp-170) REVERT: B 491 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7362 (mtpt) REVERT: B 497 LYS cc_start: 0.8299 (tppt) cc_final: 0.7973 (tppt) outliers start: 62 outliers final: 32 residues processed: 351 average time/residue: 1.3407 time to fit residues: 505.1738 Evaluate side-chains 349 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 313 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 96 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 111 optimal weight: 0.0020 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN A 459 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.125493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112734 restraints weight = 15424.179| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.68 r_work: 0.3489 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12021 Z= 0.174 Angle : 0.533 9.247 16290 Z= 0.285 Chirality : 0.043 0.278 1770 Planarity : 0.004 0.035 2097 Dihedral : 6.539 78.900 1787 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.88 % Allowed : 26.43 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.22), residues: 1452 helix: 2.56 (0.27), residues: 378 sheet: 0.53 (0.30), residues: 333 loop : -1.28 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 65 HIS 0.011 0.001 HIS C 356 PHE 0.023 0.002 PHE C 339 TYR 0.026 0.002 TYR A 489 ARG 0.007 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 9) link_NAG-ASN : angle 2.03837 ( 27) hydrogen bonds : bond 0.05455 ( 462) hydrogen bonds : angle 4.85088 ( 1356) SS BOND : bond 0.00476 ( 18) SS BOND : angle 1.33541 ( 36) covalent geometry : bond 0.00413 (11994) covalent geometry : angle 0.52422 (16227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 307 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 ASP cc_start: 0.7970 (t0) cc_final: 0.7593 (t0) REVERT: B 436 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7442 (mpp-170) REVERT: B 491 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7310 (mtpt) REVERT: B 497 LYS cc_start: 0.8317 (tppt) cc_final: 0.7984 (tppt) outliers start: 63 outliers final: 32 residues processed: 342 average time/residue: 1.3031 time to fit residues: 478.7363 Evaluate side-chains 345 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 311 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 0.0370 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 142 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 224 ASN A 380 ASN B 224 ASN B 296 HIS B 459 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.126348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.113547 restraints weight = 15545.610| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.70 r_work: 0.3502 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12021 Z= 0.129 Angle : 0.500 8.184 16290 Z= 0.268 Chirality : 0.042 0.270 1770 Planarity : 0.004 0.035 2097 Dihedral : 5.525 55.428 1771 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.57 % Allowed : 27.05 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1452 helix: 2.65 (0.27), residues: 378 sheet: 0.57 (0.30), residues: 333 loop : -1.24 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 422 HIS 0.011 0.001 HIS C 356 PHE 0.024 0.001 PHE C 339 TYR 0.028 0.001 TYR A 489 ARG 0.006 0.000 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 9) link_NAG-ASN : angle 1.93010 ( 27) hydrogen bonds : bond 0.04960 ( 462) hydrogen bonds : angle 4.70190 ( 1356) SS BOND : bond 0.00423 ( 18) SS BOND : angle 1.24402 ( 36) covalent geometry : bond 0.00297 (11994) covalent geometry : angle 0.49176 (16227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 313 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8423 (p) cc_final: 0.8189 (t) REVERT: A 345 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: A 456 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 458 ASP cc_start: 0.7973 (t0) cc_final: 0.7688 (t0) REVERT: A 479 MET cc_start: 0.7998 (tpp) cc_final: 0.7513 (mmp) REVERT: B 436 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7458 (mpp-170) REVERT: B 491 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7278 (mtpt) REVERT: B 497 LYS cc_start: 0.8320 (tppt) cc_final: 0.7994 (tppt) outliers start: 59 outliers final: 36 residues processed: 345 average time/residue: 1.2715 time to fit residues: 472.3132 Evaluate side-chains 346 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 306 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 114 optimal weight: 0.6980 chunk 101 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN B 224 ASN B 296 HIS B 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.126799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.113998 restraints weight = 15697.578| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.71 r_work: 0.3508 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12021 Z= 0.116 Angle : 0.488 7.577 16290 Z= 0.261 Chirality : 0.042 0.264 1770 Planarity : 0.004 0.034 2097 Dihedral : 5.358 55.284 1771 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.34 % Allowed : 27.75 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.23), residues: 1452 helix: 2.74 (0.27), residues: 378 sheet: 0.62 (0.30), residues: 333 loop : -1.21 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 422 HIS 0.011 0.001 HIS C 356 PHE 0.025 0.001 PHE C 339 TYR 0.028 0.001 TYR A 489 ARG 0.007 0.000 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 9) link_NAG-ASN : angle 1.85501 ( 27) hydrogen bonds : bond 0.04756 ( 462) hydrogen bonds : angle 4.61285 ( 1356) SS BOND : bond 0.00392 ( 18) SS BOND : angle 1.19465 ( 36) covalent geometry : bond 0.00266 (11994) covalent geometry : angle 0.48014 (16227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 314 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8403 (p) cc_final: 0.8183 (t) REVERT: C 341 GLU cc_start: 0.7168 (mp0) cc_final: 0.6928 (mp0) REVERT: A 345 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: A 440 PHE cc_start: 0.8084 (t80) cc_final: 0.7739 (t80) REVERT: A 456 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 479 MET cc_start: 0.8009 (tpp) cc_final: 0.7528 (mmp) REVERT: B 436 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7440 (mpp-170) REVERT: B 491 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7263 (mtpt) REVERT: B 497 LYS cc_start: 0.8321 (tppt) cc_final: 0.7985 (tppt) outliers start: 56 outliers final: 33 residues processed: 345 average time/residue: 1.3097 time to fit residues: 486.6482 Evaluate side-chains 350 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 124 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN B 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.125693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113323 restraints weight = 15700.117| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.61 r_work: 0.3506 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12021 Z= 0.133 Angle : 0.507 7.658 16290 Z= 0.271 Chirality : 0.042 0.262 1770 Planarity : 0.004 0.035 2097 Dihedral : 5.316 54.502 1771 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.03 % Allowed : 28.37 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1452 helix: 2.71 (0.27), residues: 378 sheet: 0.63 (0.30), residues: 333 loop : -1.22 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.011 0.001 HIS C 356 PHE 0.026 0.001 PHE C 339 TYR 0.029 0.001 TYR A 489 ARG 0.007 0.000 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 9) link_NAG-ASN : angle 1.86646 ( 27) hydrogen bonds : bond 0.04881 ( 462) hydrogen bonds : angle 4.61470 ( 1356) SS BOND : bond 0.00410 ( 18) SS BOND : angle 1.22854 ( 36) covalent geometry : bond 0.00311 (11994) covalent geometry : angle 0.49892 (16227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8421 (p) cc_final: 0.8197 (t) REVERT: C 341 GLU cc_start: 0.7169 (mp0) cc_final: 0.6930 (mp0) REVERT: A 345 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: A 456 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 479 MET cc_start: 0.8003 (tpp) cc_final: 0.7537 (mmp) REVERT: B 186 ASN cc_start: 0.8489 (t0) cc_final: 0.8206 (t0) REVERT: B 436 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7388 (mpp-170) REVERT: B 491 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7214 (mtpt) outliers start: 52 outliers final: 36 residues processed: 333 average time/residue: 1.3193 time to fit residues: 472.0181 Evaluate side-chains 344 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 283 GLN C 356 HIS A 380 ASN A 459 ASN B 89 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.125445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113125 restraints weight = 15627.633| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.61 r_work: 0.3500 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12021 Z= 0.148 Angle : 0.515 7.882 16290 Z= 0.276 Chirality : 0.043 0.263 1770 Planarity : 0.004 0.036 2097 Dihedral : 5.212 55.306 1766 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.88 % Allowed : 28.37 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1452 helix: 2.67 (0.27), residues: 378 sheet: 0.62 (0.30), residues: 333 loop : -1.25 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.012 0.001 HIS C 356 PHE 0.028 0.002 PHE C 339 TYR 0.026 0.001 TYR A 489 ARG 0.007 0.000 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 9) link_NAG-ASN : angle 1.88854 ( 27) hydrogen bonds : bond 0.05036 ( 462) hydrogen bonds : angle 4.64487 ( 1356) SS BOND : bond 0.00432 ( 18) SS BOND : angle 1.26101 ( 36) covalent geometry : bond 0.00348 (11994) covalent geometry : angle 0.50711 (16227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8432 (p) cc_final: 0.8187 (t) REVERT: C 341 GLU cc_start: 0.7200 (mp0) cc_final: 0.6942 (mp0) REVERT: C 479 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7279 (mtt) REVERT: A 345 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: A 479 MET cc_start: 0.8019 (tpp) cc_final: 0.7553 (mmp) REVERT: B 186 ASN cc_start: 0.8498 (t0) cc_final: 0.8200 (t0) REVERT: B 436 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7405 (mpp-170) REVERT: B 491 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7241 (mtpt) outliers start: 50 outliers final: 36 residues processed: 329 average time/residue: 1.3076 time to fit residues: 462.2777 Evaluate side-chains 346 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 306 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 296 HIS B 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113763 restraints weight = 15698.139| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.60 r_work: 0.3517 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12021 Z= 0.119 Angle : 0.507 7.387 16290 Z= 0.269 Chirality : 0.042 0.258 1770 Planarity : 0.004 0.035 2097 Dihedral : 5.114 54.360 1765 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.49 % Allowed : 28.60 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1452 helix: 2.73 (0.27), residues: 378 sheet: 0.62 (0.32), residues: 303 loop : -1.10 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.004 0.001 HIS A 13 PHE 0.027 0.001 PHE C 339 TYR 0.030 0.001 TYR A 489 ARG 0.007 0.000 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 9) link_NAG-ASN : angle 1.80391 ( 27) hydrogen bonds : bond 0.04730 ( 462) hydrogen bonds : angle 4.58313 ( 1356) SS BOND : bond 0.00396 ( 18) SS BOND : angle 1.19917 ( 36) covalent geometry : bond 0.00275 (11994) covalent geometry : angle 0.49902 (16227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 304 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 292 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.7503 (t) REVERT: C 302 THR cc_start: 0.8412 (p) cc_final: 0.8200 (t) REVERT: C 341 GLU cc_start: 0.7227 (mp0) cc_final: 0.6957 (mp0) REVERT: C 479 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7257 (mtt) REVERT: A 345 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: A 479 MET cc_start: 0.8001 (tpp) cc_final: 0.7559 (mmp) REVERT: B 186 ASN cc_start: 0.8510 (t0) cc_final: 0.8223 (t0) REVERT: B 436 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7417 (mpp-170) REVERT: B 491 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7236 (mtpt) outliers start: 45 outliers final: 35 residues processed: 327 average time/residue: 1.3222 time to fit residues: 464.3201 Evaluate side-chains 337 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN A 459 ASN B 89 ASN B 224 ASN B 244 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112101 restraints weight = 15898.869| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.58 r_work: 0.3497 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12021 Z= 0.185 Angle : 0.551 8.543 16290 Z= 0.293 Chirality : 0.044 0.265 1770 Planarity : 0.004 0.036 2097 Dihedral : 5.228 55.348 1765 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.18 % Allowed : 29.15 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.22), residues: 1452 helix: 2.59 (0.27), residues: 378 sheet: 0.60 (0.31), residues: 303 loop : -1.20 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 65 HIS 0.004 0.001 HIS C 13 PHE 0.029 0.002 PHE C 339 TYR 0.027 0.002 TYR A 489 ARG 0.007 0.000 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 9) link_NAG-ASN : angle 1.94297 ( 27) hydrogen bonds : bond 0.05346 ( 462) hydrogen bonds : angle 4.72213 ( 1356) SS BOND : bond 0.00477 ( 18) SS BOND : angle 1.32121 ( 36) covalent geometry : bond 0.00442 (11994) covalent geometry : angle 0.54258 (16227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 5.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 341 GLU cc_start: 0.7241 (mp0) cc_final: 0.6962 (mp0) REVERT: C 479 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7252 (mtt) REVERT: A 345 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: A 479 MET cc_start: 0.8038 (tpp) cc_final: 0.7583 (mmp) REVERT: B 186 ASN cc_start: 0.8529 (t0) cc_final: 0.8241 (t0) REVERT: B 436 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7407 (mpp-170) REVERT: B 491 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7214 (mtpt) outliers start: 41 outliers final: 34 residues processed: 322 average time/residue: 1.3480 time to fit residues: 468.4022 Evaluate side-chains 337 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.125001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113073 restraints weight = 15879.601| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.57 r_work: 0.3505 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12021 Z= 0.133 Angle : 0.532 9.530 16290 Z= 0.282 Chirality : 0.042 0.261 1770 Planarity : 0.004 0.036 2097 Dihedral : 5.156 54.561 1765 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.41 % Allowed : 28.84 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.22), residues: 1452 helix: 2.64 (0.27), residues: 378 sheet: 0.65 (0.32), residues: 303 loop : -1.15 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 422 HIS 0.010 0.001 HIS C 356 PHE 0.030 0.002 PHE C 339 TYR 0.028 0.001 TYR A 489 ARG 0.007 0.000 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 9) link_NAG-ASN : angle 1.83265 ( 27) hydrogen bonds : bond 0.04932 ( 462) hydrogen bonds : angle 4.63585 ( 1356) SS BOND : bond 0.00427 ( 18) SS BOND : angle 1.24002 ( 36) covalent geometry : bond 0.00311 (11994) covalent geometry : angle 0.52408 (16227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10783.92 seconds wall clock time: 185 minutes 48.35 seconds (11148.35 seconds total)