Starting phenix.real_space_refine on Tue Jul 29 22:09:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhf_38349/07_2025/8xhf_38349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhf_38349/07_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_38349/07_2025/8xhf_38349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhf_38349/07_2025/8xhf_38349.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhf_38349/07_2025/8xhf_38349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhf_38349/07_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-5711/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: 7.78, 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 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: 1.58 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: 3.75 Time building geometry restraints manager: 3.17 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: 0.010 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.260 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.370 ------------------------------------------------------------------------------- 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 : 1.218 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: 1.4129 time to fit residues: 534.7859 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 : 1.267 ------------------------------------------------------------------------------- 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 = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114288 restraints weight = 15480.484| |-----------------------------------------------------------------------------| r_work (start): 0.3603 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: 3.65 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 64.852 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 1.78377 ( 27) hydrogen bonds : bond 0.05155 ( 462) hydrogen bonds : angle 5.09783 ( 1356) SS BOND : bond 0.00551 ( 18) SS BOND : angle 1.37178 ( 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 : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8476 (p) cc_final: 0.8249 (t) REVERT: C 491 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7612 (tttm) REVERT: A 67 LEU cc_start: 0.8770 (mt) cc_final: 0.8491 (mt) REVERT: A 456 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 479 MET cc_start: 0.7973 (tpp) cc_final: 0.7486 (mmp) REVERT: B 491 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7364 (mtpt) outliers start: 74 outliers final: 35 residues processed: 364 average time/residue: 1.4165 time to fit residues: 552.8333 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 : 1.285 ------------------------------------------------------------------------------- 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: 0.4980 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 143 optimal weight: 0.0870 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 chunk 14 optimal weight: 0.4980 overall best weight: 0.2308 ------------------------------------------------------------------------------- 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 186 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 = 0.3815 r_free = 0.3815 target = 0.128640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115837 restraints weight = 15630.287| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.70 r_work: 0.3534 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12021 Z= 0.097 Angle : 0.472 8.060 16290 Z= 0.252 Chirality : 0.041 0.246 1770 Planarity : 0.004 0.034 2097 Dihedral : 6.592 73.594 1793 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.57 % Allowed : 26.43 % Favored : 68.99 % 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: 0.50 (0.23), residues: 1452 helix: 2.78 (0.27), residues: 378 sheet: 0.59 (0.31), residues: 318 loop : -1.13 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 422 HIS 0.010 0.001 HIS C 356 PHE 0.022 0.001 PHE C 339 TYR 0.008 0.001 TYR A 12 ARG 0.007 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 9) link_NAG-ASN : angle 1.80586 ( 27) hydrogen bonds : bond 0.04499 ( 462) hydrogen bonds : angle 4.72032 ( 1356) SS BOND : bond 0.00401 ( 18) SS BOND : angle 1.10065 ( 36) covalent geometry : bond 0.00204 (11994) covalent geometry : angle 0.46420 (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: 59 poor density : 322 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 458 ASP cc_start: 0.7947 (t0) cc_final: 0.7641 (t0) REVERT: A 479 MET cc_start: 0.7988 (tpp) cc_final: 0.7513 (mmp) REVERT: B 436 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7330 (mpp-170) REVERT: B 491 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7371 (mtpt) REVERT: B 497 LYS cc_start: 0.8273 (tppt) cc_final: 0.7947 (tppt) outliers start: 59 outliers final: 22 residues processed: 357 average time/residue: 1.2755 time to fit residues: 489.8048 Evaluate side-chains 333 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 308 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 321 LEU 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 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 292 THR 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 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 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: 4.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 122 optimal weight: 0.0270 chunk 111 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 360 GLN B 459 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.127100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114280 restraints weight = 15474.172| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.69 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: 0.8118 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 : 0.003 0.040 12021 Z= 0.136 Angle : 0.494 8.542 16290 Z= 0.264 Chirality : 0.042 0.261 1770 Planarity : 0.004 0.033 2097 Dihedral : 5.875 87.467 1773 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.65 % Allowed : 27.13 % Favored : 68.22 % 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: 2.75 (0.27), residues: 378 sheet: 0.61 (0.30), residues: 333 loop : -1.18 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.011 0.001 HIS C 356 PHE 0.022 0.001 PHE C 339 TYR 0.016 0.001 TYR A 12 ARG 0.007 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 9) link_NAG-ASN : angle 1.88314 ( 27) hydrogen bonds : bond 0.04866 ( 462) hydrogen bonds : angle 4.68878 ( 1356) SS BOND : bond 0.00427 ( 18) SS BOND : angle 1.21322 ( 36) covalent geometry : bond 0.00316 (11994) covalent geometry : angle 0.48585 (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 374 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 314 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8423 (mp) REVERT: A 458 ASP cc_start: 0.7963 (t0) cc_final: 0.7650 (t0) REVERT: A 479 MET cc_start: 0.8013 (tpp) cc_final: 0.7548 (mmp) REVERT: B 436 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7439 (mpp-170) REVERT: B 491 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7327 (mtpt) REVERT: B 497 LYS cc_start: 0.8300 (tppt) cc_final: 0.7979 (tppt) outliers start: 60 outliers final: 34 residues processed: 348 average time/residue: 1.4526 time to fit residues: 543.7842 Evaluate side-chains 346 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 309 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 213 SER 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 497 LYS 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 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 394 GLU Chi-restraints excluded: chain A residue 410 LEU 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 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 454 MET 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: 1.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 142 optimal weight: 5.9990 chunk 125 optimal weight: 0.0070 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.128037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.115292 restraints weight = 15597.091| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.70 r_work: 0.3529 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12021 Z= 0.102 Angle : 0.473 7.313 16290 Z= 0.252 Chirality : 0.041 0.256 1770 Planarity : 0.004 0.033 2097 Dihedral : 5.220 53.795 1771 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.11 % Allowed : 27.67 % Favored : 68.22 % 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: 0.58 (0.23), residues: 1452 helix: 2.84 (0.27), residues: 378 sheet: 0.67 (0.30), residues: 333 loop : -1.13 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 422 HIS 0.011 0.001 HIS C 356 PHE 0.024 0.001 PHE C 339 TYR 0.011 0.001 TYR A 12 ARG 0.006 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 9) link_NAG-ASN : angle 1.76650 ( 27) hydrogen bonds : bond 0.04420 ( 462) hydrogen bonds : angle 4.53333 ( 1356) SS BOND : bond 0.00365 ( 18) SS BOND : angle 1.13264 ( 36) covalent geometry : bond 0.00227 (11994) covalent geometry : angle 0.46487 (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 355 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 302 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 479 MET cc_start: 0.7978 (tpp) cc_final: 0.7522 (mmp) REVERT: B 436 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7425 (mpp-170) REVERT: B 491 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7298 (mtpt) REVERT: B 497 LYS cc_start: 0.8298 (tppt) cc_final: 0.7969 (tppt) outliers start: 53 outliers final: 32 residues processed: 331 average time/residue: 1.8378 time to fit residues: 655.0029 Evaluate side-chains 339 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 321 LEU 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 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 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 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 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 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 276 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS A 380 ASN B 160 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 = 0.3794 r_free = 0.3794 target = 0.126952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114164 restraints weight = 15696.082| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.71 r_work: 0.3509 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12021 Z= 0.131 Angle : 0.495 7.660 16290 Z= 0.264 Chirality : 0.042 0.258 1770 Planarity : 0.004 0.033 2097 Dihedral : 5.151 54.515 1769 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.19 % Allowed : 28.29 % Favored : 67.52 % 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: 0.55 (0.23), residues: 1452 helix: 2.82 (0.27), residues: 378 sheet: 0.67 (0.30), residues: 333 loop : -1.17 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.011 0.001 HIS C 356 PHE 0.020 0.001 PHE A 295 TYR 0.028 0.001 TYR A 489 ARG 0.007 0.001 ARG A 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 9) link_NAG-ASN : angle 1.82956 ( 27) hydrogen bonds : bond 0.04757 ( 462) hydrogen bonds : angle 4.57605 ( 1356) SS BOND : bond 0.00411 ( 18) SS BOND : angle 1.19424 ( 36) covalent geometry : bond 0.00306 (11994) covalent geometry : angle 0.48726 (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 358 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 MET cc_start: 0.8021 (tpp) cc_final: 0.7568 (mmp) REVERT: B 436 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7452 (mpp-170) REVERT: B 491 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7259 (mtpt) REVERT: B 497 LYS cc_start: 0.8333 (tppt) cc_final: 0.7991 (tppt) outliers start: 54 outliers final: 35 residues processed: 335 average time/residue: 1.6168 time to fit residues: 589.0285 Evaluate side-chains 340 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE 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 478 CYS Chi-restraints excluded: chain C residue 497 LYS 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 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 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 463 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 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: 0.9980 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS A 380 ASN A 459 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.112968 restraints weight = 15693.456| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.63 r_work: 0.3497 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1238 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= 0.163 Angle : 0.525 7.989 16290 Z= 0.279 Chirality : 0.043 0.264 1770 Planarity : 0.004 0.034 2097 Dihedral : 5.190 54.289 1768 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.57 % Allowed : 29.07 % Favored : 67.36 % 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: 0.48 (0.23), residues: 1452 helix: 2.75 (0.27), residues: 378 sheet: 0.58 (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 65 HIS 0.012 0.001 HIS C 356 PHE 0.022 0.002 PHE A 295 TYR 0.029 0.002 TYR A 489 ARG 0.007 0.001 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 9) link_NAG-ASN : angle 1.90142 ( 27) hydrogen bonds : bond 0.05104 ( 462) hydrogen bonds : angle 4.65909 ( 1356) SS BOND : bond 0.00467 ( 18) SS BOND : angle 1.26374 ( 36) covalent geometry : bond 0.00389 (11994) covalent geometry : angle 0.51663 (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 346 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: A 479 MET cc_start: 0.8026 (tpp) cc_final: 0.7560 (mmp) REVERT: B 186 ASN cc_start: 0.8492 (t0) cc_final: 0.8212 (t0) REVERT: B 436 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7406 (mpp-170) REVERT: B 491 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7281 (mtpt) outliers start: 46 outliers final: 34 residues processed: 324 average time/residue: 1.8430 time to fit residues: 642.0999 Evaluate side-chains 335 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE 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 478 CYS 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 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 454 MET Chi-restraints excluded: chain A residue 463 LEU 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 228 SER Chi-restraints excluded: chain B residue 236 LEU 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: 0.7980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS A 380 ASN B 224 ASN B 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.123424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.111419 restraints weight = 15997.367| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.59 r_work: 0.3484 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12021 Z= 0.227 Angle : 0.574 9.006 16290 Z= 0.306 Chirality : 0.046 0.279 1770 Planarity : 0.004 0.037 2097 Dihedral : 5.251 52.997 1763 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 3.64 % Allowed : 28.60 % 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: 0.29 (0.22), residues: 1452 helix: 2.54 (0.27), residues: 378 sheet: 0.50 (0.31), residues: 303 loop : -1.21 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 344 HIS 0.012 0.001 HIS C 356 PHE 0.032 0.002 PHE B 440 TYR 0.029 0.002 TYR A 489 ARG 0.007 0.001 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 9) link_NAG-ASN : angle 2.10330 ( 27) hydrogen bonds : bond 0.05735 ( 462) hydrogen bonds : angle 4.81878 ( 1356) SS BOND : bond 0.00537 ( 18) SS BOND : angle 1.38696 ( 36) covalent geometry : bond 0.00547 (11994) covalent geometry : angle 0.56516 (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 348 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 479 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7229 (mtt) REVERT: A 345 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: B 436 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7419 (mpp-170) REVERT: B 491 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7258 (mtpt) outliers start: 47 outliers final: 31 residues processed: 324 average time/residue: 1.3835 time to fit residues: 480.0326 Evaluate side-chains 342 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 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 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 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 463 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 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: 0.5980 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 7 optimal weight: 0.1980 chunk 121 optimal weight: 0.0870 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.126333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113999 restraints weight = 15702.812| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.61 r_work: 0.3520 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12021 Z= 0.108 Angle : 0.499 7.190 16290 Z= 0.265 Chirality : 0.041 0.259 1770 Planarity : 0.004 0.033 2097 Dihedral : 5.036 52.353 1763 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.41 % Allowed : 28.91 % 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: 0.49 (0.23), residues: 1452 helix: 2.74 (0.28), residues: 378 sheet: 0.61 (0.32), residues: 303 loop : -1.10 (0.21), residues: 771 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 0.025 0.001 PHE C 339 TYR 0.029 0.001 TYR A 489 ARG 0.007 0.000 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 9) link_NAG-ASN : angle 1.78996 ( 27) hydrogen bonds : bond 0.04620 ( 462) hydrogen bonds : angle 4.58079 ( 1356) SS BOND : bond 0.00386 ( 18) SS BOND : angle 1.20259 ( 36) covalent geometry : bond 0.00241 (11994) covalent geometry : angle 0.49137 (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 338 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8421 (p) cc_final: 0.8212 (t) REVERT: A 345 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: A 479 MET cc_start: 0.8036 (tpp) cc_final: 0.7593 (mmp) REVERT: B 186 ASN cc_start: 0.8470 (t0) cc_final: 0.8259 (t0) REVERT: B 436 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7401 (mpp-170) REVERT: B 491 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7225 (mtpt) outliers start: 44 outliers final: 32 residues processed: 315 average time/residue: 1.3152 time to fit residues: 446.9268 Evaluate side-chains 330 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 295 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 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 389 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS 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 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 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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 = 0.3767 r_free = 0.3767 target = 0.124802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112885 restraints weight = 15902.501| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.57 r_work: 0.3507 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1336 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= 0.150 Angle : 0.534 9.276 16290 Z= 0.282 Chirality : 0.043 0.260 1770 Planarity : 0.004 0.035 2097 Dihedral : 5.083 53.203 1763 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.87 % Allowed : 29.92 % Favored : 67.21 % 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: 2.66 (0.27), residues: 378 sheet: 0.58 (0.31), residues: 303 loop : -1.14 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 65 HIS 0.015 0.001 HIS C 356 PHE 0.027 0.002 PHE C 339 TYR 0.026 0.001 TYR A 489 ARG 0.007 0.001 ARG C 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 9) link_NAG-ASN : angle 1.87638 ( 27) hydrogen bonds : bond 0.05031 ( 462) hydrogen bonds : angle 4.64538 ( 1356) SS BOND : bond 0.00445 ( 18) SS BOND : angle 1.29650 ( 36) covalent geometry : bond 0.00354 (11994) covalent geometry : angle 0.52582 (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 332 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8442 (p) cc_final: 0.8209 (t) REVERT: A 345 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: A 479 MET cc_start: 0.8060 (tpp) cc_final: 0.7633 (mmp) REVERT: B 436 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7375 (mpp-170) REVERT: B 491 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7222 (mtpt) outliers start: 37 outliers final: 32 residues processed: 315 average time/residue: 1.2931 time to fit residues: 437.3372 Evaluate side-chains 331 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 296 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 478 CYS 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 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 463 LEU Chi-restraints excluded: chain B residue 110 LEU 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 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: 2.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.123770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.111511 restraints weight = 15495.907| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.60 r_work: 0.3484 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12021 Z= 0.237 Angle : 0.601 11.320 16290 Z= 0.318 Chirality : 0.046 0.272 1770 Planarity : 0.004 0.036 2097 Dihedral : 5.284 54.901 1763 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 3.18 % Allowed : 29.84 % Favored : 66.98 % 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: 0.23 (0.22), residues: 1452 helix: 2.45 (0.27), residues: 378 sheet: 0.51 (0.31), residues: 303 loop : -1.25 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 422 HIS 0.009 0.001 HIS C 356 PHE 0.033 0.002 PHE B 440 TYR 0.031 0.002 TYR A 489 ARG 0.008 0.001 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 9) link_NAG-ASN : angle 2.06822 ( 27) hydrogen bonds : bond 0.05754 ( 462) hydrogen bonds : angle 4.82200 ( 1356) SS BOND : bond 0.00548 ( 18) SS BOND : angle 1.41047 ( 36) covalent geometry : bond 0.00573 (11994) covalent geometry : angle 0.59215 (16227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12269.81 seconds wall clock time: 219 minutes 5.21 seconds (13145.21 seconds total)