Starting phenix.real_space_refine on Wed Sep 17 22:11:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhf_38349/09_2025/8xhf_38349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhf_38349/09_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_38349/09_2025/8xhf_38349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhf_38349/09_2025/8xhf_38349.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhf_38349/09_2025/8xhf_38349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhf_38349/09_2025/8xhf_38349.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.95, per 1000 atoms: 0.25 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: 1.02 Conformation dependent library (CDL) restraints added in 541.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.45 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: 1.97 Time building geometry restraints manager: 1.41 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 602) selection = chain 'B' selection = (chain 'C' and resid 6 through 602) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.590 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 192 TYR 0.018 0.001 TYR A 12 PHE 0.030 0.002 PHE C 339 TRP 0.010 0.001 TRP C 422 HIS 0.012 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00397 (11994) covalent geometry : angle 0.52641 (16227) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.26767 ( 36) hydrogen bonds : bond 0.17671 ( 462) hydrogen bonds : angle 6.96667 ( 1356) link_NAG-ASN : bond 0.00272 ( 9) link_NAG-ASN : angle 1.79231 ( 27) *********************** 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 : 0.359 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: 0.6653 time to fit residues: 251.7658 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 : 0.597 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 499 ASN A 380 ASN A 392 GLN B 186 ASN B 224 ASN 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 = 0.3749 r_free = 0.3749 target = 0.123792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111008 restraints weight = 15564.458| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.69 r_work: 0.3464 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12021 Z= 0.268 Angle : 0.609 9.264 16290 Z= 0.326 Chirality : 0.047 0.274 1770 Planarity : 0.005 0.039 2097 Dihedral : 8.575 70.378 1845 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 6.12 % Allowed : 25.19 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.22), residues: 1452 helix: 2.05 (0.27), residues: 378 sheet: 0.41 (0.30), residues: 333 loop : -1.49 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 126 TYR 0.024 0.002 TYR A 12 PHE 0.035 0.002 PHE B 440 TRP 0.011 0.002 TRP C 422 HIS 0.011 0.002 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00647 (11994) covalent geometry : angle 0.59904 (16227) SS BOND : bond 0.00511 ( 18) SS BOND : angle 1.69769 ( 36) hydrogen bonds : bond 0.06512 ( 462) hydrogen bonds : angle 5.29810 ( 1356) link_NAG-ASN : bond 0.00339 ( 9) link_NAG-ASN : angle 2.12205 ( 27) *********************** 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 395 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 316 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8256 (mtpt) REVERT: C 272 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: B 436 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7438 (mpp-170) REVERT: B 491 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7434 (mtpt) REVERT: B 497 LYS cc_start: 0.8340 (tppt) cc_final: 0.8137 (tppt) outliers start: 79 outliers final: 43 residues processed: 366 average time/residue: 0.6697 time to fit residues: 262.2258 Evaluate side-chains 359 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 312 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 48 LYS 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 272 GLU 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 345 GLN Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain C residue 407 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 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 213 SER 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 311 LYS Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 136 SER 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 293 LEU Chi-restraints excluded: chain B residue 368 LYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 459 ASN B 472 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.125301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112434 restraints weight = 15675.715| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.70 r_work: 0.3486 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12021 Z= 0.156 Angle : 0.538 10.951 16290 Z= 0.287 Chirality : 0.043 0.282 1770 Planarity : 0.004 0.038 2097 Dihedral : 7.197 60.011 1795 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Rotamer: Outliers : 5.43 % Allowed : 25.43 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.22), residues: 1452 helix: 2.36 (0.27), residues: 378 sheet: 0.53 (0.30), residues: 333 loop : -1.38 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.017 0.001 TYR A 12 PHE 0.021 0.002 PHE A 295 TRP 0.010 0.001 TRP C 422 HIS 0.014 0.001 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00367 (11994) covalent geometry : angle 0.52779 (16227) SS BOND : bond 0.00508 ( 18) SS BOND : angle 1.41653 ( 36) hydrogen bonds : bond 0.05562 ( 462) hydrogen bonds : angle 4.99314 ( 1356) link_NAG-ASN : bond 0.00301 ( 9) link_NAG-ASN : angle 2.12798 ( 27) *********************** 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 389 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: B 468 PHE cc_start: 0.8216 (m-80) cc_final: 0.7976 (m-80) REVERT: B 491 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7357 (mtpt) REVERT: B 497 LYS cc_start: 0.8328 (tppt) cc_final: 0.7987 (tppt) outliers start: 70 outliers final: 43 residues processed: 358 average time/residue: 0.6685 time to fit residues: 255.9059 Evaluate side-chains 359 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU 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 360 GLN Chi-restraints excluded: chain C residue 407 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 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 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 LYS 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 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.125169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112399 restraints weight = 15628.454| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.69 r_work: 0.3486 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12021 Z= 0.162 Angle : 0.535 9.155 16290 Z= 0.285 Chirality : 0.043 0.285 1770 Planarity : 0.004 0.038 2097 Dihedral : 6.565 59.347 1786 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.81 % Allowed : 26.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1452 helix: 2.44 (0.27), residues: 378 sheet: 0.52 (0.30), residues: 333 loop : -1.36 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.029 0.002 TYR A 489 PHE 0.024 0.002 PHE C 339 TRP 0.010 0.001 TRP C 422 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00382 (11994) covalent geometry : angle 0.52503 (16227) SS BOND : bond 0.00439 ( 18) SS BOND : angle 1.34757 ( 36) hydrogen bonds : bond 0.05438 ( 462) hydrogen bonds : angle 4.87164 ( 1356) link_NAG-ASN : bond 0.00315 ( 9) link_NAG-ASN : angle 2.07785 ( 27) *********************** 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 376 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 341 GLU cc_start: 0.7147 (mp0) cc_final: 0.6936 (mp0) REVERT: A 345 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: A 456 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 468 PHE cc_start: 0.8143 (m-80) cc_final: 0.7899 (m-80) REVERT: B 491 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7296 (mtpt) REVERT: B 497 LYS cc_start: 0.8316 (tppt) cc_final: 0.7982 (tppt) outliers start: 62 outliers final: 37 residues processed: 347 average time/residue: 0.6516 time to fit residues: 242.4276 Evaluate side-chains 350 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 407 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 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 213 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 352 TYR 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 110 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 224 ASN A 380 ASN B 224 ASN B 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.125365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.112554 restraints weight = 15628.055| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.69 r_work: 0.3488 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12021 Z= 0.161 Angle : 0.531 8.582 16290 Z= 0.284 Chirality : 0.043 0.284 1770 Planarity : 0.004 0.039 2097 Dihedral : 5.919 59.307 1773 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.04 % Allowed : 26.20 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1452 helix: 2.48 (0.27), residues: 378 sheet: 0.53 (0.30), residues: 333 loop : -1.36 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 126 TYR 0.029 0.002 TYR A 489 PHE 0.025 0.002 PHE C 339 TRP 0.010 0.001 TRP C 422 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00381 (11994) covalent geometry : angle 0.52188 (16227) SS BOND : bond 0.00449 ( 18) SS BOND : angle 1.32543 ( 36) hydrogen bonds : bond 0.05381 ( 462) hydrogen bonds : angle 4.80886 ( 1356) link_NAG-ASN : bond 0.00323 ( 9) link_NAG-ASN : angle 2.07773 ( 27) *********************** 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 370 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8488 (p) cc_final: 0.8213 (t) REVERT: C 305 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: A 345 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: A 456 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8503 (mp) REVERT: B 491 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7289 (mtpt) REVERT: B 497 LYS cc_start: 0.8328 (tppt) cc_final: 0.8022 (tppt) outliers start: 65 outliers final: 41 residues processed: 340 average time/residue: 0.6337 time to fit residues: 231.0135 Evaluate side-chains 352 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 228 SER 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 345 GLN Chi-restraints excluded: chain C residue 407 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 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 111 optimal weight: 0.0010 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.126087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113277 restraints weight = 15741.926| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.70 r_work: 0.3498 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1055 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= 0.128 Angle : 0.506 7.882 16290 Z= 0.270 Chirality : 0.042 0.277 1770 Planarity : 0.004 0.038 2097 Dihedral : 5.680 58.418 1771 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.42 % Allowed : 26.90 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1452 helix: 2.59 (0.27), residues: 378 sheet: 0.57 (0.30), residues: 333 loop : -1.31 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.029 0.001 TYR A 489 PHE 0.027 0.001 PHE C 339 TRP 0.009 0.001 TRP C 422 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00296 (11994) covalent geometry : angle 0.49751 (16227) SS BOND : bond 0.00412 ( 18) SS BOND : angle 1.24498 ( 36) hydrogen bonds : bond 0.04989 ( 462) hydrogen bonds : angle 4.69372 ( 1356) link_NAG-ASN : bond 0.00317 ( 9) link_NAG-ASN : angle 1.97052 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 313 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8443 (p) cc_final: 0.8196 (t) REVERT: C 341 GLU cc_start: 0.7237 (mp0) cc_final: 0.6969 (mp0) REVERT: A 345 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: A 456 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 458 ASP cc_start: 0.7972 (t0) cc_final: 0.7655 (t0) REVERT: A 479 MET cc_start: 0.7986 (tpp) cc_final: 0.7496 (mmp) REVERT: B 491 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7276 (mtpt) REVERT: B 497 LYS cc_start: 0.8331 (tppt) cc_final: 0.8007 (tppt) outliers start: 57 outliers final: 40 residues processed: 344 average time/residue: 0.6546 time to fit residues: 241.4652 Evaluate side-chains 349 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 407 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 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 134 optimal weight: 0.0070 chunk 77 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 99 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 B 459 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.125319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113338 restraints weight = 15896.885| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.57 r_work: 0.3511 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12021 Z= 0.119 Angle : 0.505 7.456 16290 Z= 0.269 Chirality : 0.042 0.269 1770 Planarity : 0.004 0.041 2097 Dihedral : 5.340 56.423 1769 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.95 % Allowed : 27.67 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.23), residues: 1452 helix: 2.66 (0.27), residues: 378 sheet: 0.62 (0.30), residues: 333 loop : -1.27 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 192 TYR 0.028 0.001 TYR A 489 PHE 0.026 0.001 PHE C 339 TRP 0.012 0.001 TRP C 422 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00273 (11994) covalent geometry : angle 0.49698 (16227) SS BOND : bond 0.00398 ( 18) SS BOND : angle 1.24746 ( 36) hydrogen bonds : bond 0.04790 ( 462) hydrogen bonds : angle 4.64922 ( 1356) link_NAG-ASN : bond 0.00310 ( 9) link_NAG-ASN : angle 1.89985 ( 27) *********************** 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 357 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8406 (p) cc_final: 0.8191 (t) REVERT: C 341 GLU cc_start: 0.7241 (mp0) cc_final: 0.6968 (mp0) REVERT: C 479 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7276 (mtt) REVERT: A 345 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: A 456 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 458 ASP cc_start: 0.7931 (t0) cc_final: 0.7728 (t0) REVERT: A 479 MET cc_start: 0.7972 (tpp) cc_final: 0.7492 (mmp) REVERT: B 186 ASN cc_start: 0.8444 (t0) cc_final: 0.8201 (t0) REVERT: B 436 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7317 (mpp-170) REVERT: B 491 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7234 (mtpt) outliers start: 51 outliers final: 35 residues processed: 332 average time/residue: 0.6641 time to fit residues: 236.4727 Evaluate side-chains 346 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 306 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 407 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 479 MET Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 13 HIS 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 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 440 PHE 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 107 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.125715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113496 restraints weight = 15548.417| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.58 r_work: 0.3510 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1222 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= 0.125 Angle : 0.503 7.360 16290 Z= 0.268 Chirality : 0.042 0.266 1770 Planarity : 0.004 0.038 2097 Dihedral : 5.235 55.241 1769 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.42 % Allowed : 27.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.23), residues: 1452 helix: 2.66 (0.27), residues: 378 sheet: 0.56 (0.32), residues: 303 loop : -1.13 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.026 0.001 TYR A 489 PHE 0.027 0.001 PHE C 339 TRP 0.018 0.001 TRP C 422 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00289 (11994) covalent geometry : angle 0.49457 (16227) SS BOND : bond 0.00390 ( 18) SS BOND : angle 1.22952 ( 36) hydrogen bonds : bond 0.04816 ( 462) hydrogen bonds : angle 4.62214 ( 1356) link_NAG-ASN : bond 0.00308 ( 9) link_NAG-ASN : angle 1.88291 ( 27) *********************** 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 369 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 312 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8398 (p) cc_final: 0.8178 (t) REVERT: C 341 GLU cc_start: 0.7283 (mp0) cc_final: 0.6995 (mp0) REVERT: A 345 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: A 456 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 458 ASP cc_start: 0.7931 (t0) cc_final: 0.7726 (t0) REVERT: A 479 MET cc_start: 0.7984 (tpp) cc_final: 0.7514 (mmp) REVERT: B 186 ASN cc_start: 0.8460 (t0) cc_final: 0.8200 (t0) REVERT: B 436 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7323 (mpp-170) REVERT: B 491 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7181 (mtpt) outliers start: 57 outliers final: 39 residues processed: 340 average time/residue: 0.6360 time to fit residues: 231.9552 Evaluate side-chains 350 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 307 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 407 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 A residue 13 HIS 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 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 352 TYR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 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 292 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 341 GLU 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 440 PHE 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 3 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 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 = 0.3749 r_free = 0.3749 target = 0.123584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.110813 restraints weight = 15568.947| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.69 r_work: 0.3461 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12021 Z= 0.296 Angle : 0.624 9.228 16290 Z= 0.333 Chirality : 0.048 0.289 1770 Planarity : 0.004 0.040 2097 Dihedral : 5.444 57.077 1764 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 3.72 % Allowed : 28.29 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.22), residues: 1452 helix: 2.31 (0.27), residues: 378 sheet: 0.44 (0.31), residues: 303 loop : -1.33 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 126 TYR 0.037 0.002 TYR A 489 PHE 0.040 0.003 PHE B 440 TRP 0.013 0.002 TRP C 65 HIS 0.007 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00719 (11994) covalent geometry : angle 0.61428 (16227) SS BOND : bond 0.00573 ( 18) SS BOND : angle 1.48563 ( 36) hydrogen bonds : bond 0.06172 ( 462) hydrogen bonds : angle 4.94782 ( 1356) link_NAG-ASN : bond 0.00383 ( 9) link_NAG-ASN : angle 2.26732 ( 27) *********************** 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 351 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: C 341 GLU cc_start: 0.7330 (mp0) cc_final: 0.7032 (mp0) REVERT: C 362 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7562 (p) REVERT: C 479 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7377 (mmm) REVERT: A 345 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: A 458 ASP cc_start: 0.7998 (t0) cc_final: 0.7649 (t0) REVERT: B 436 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7520 (mpp-170) REVERT: B 491 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7296 (mtpt) outliers start: 48 outliers final: 34 residues processed: 329 average time/residue: 0.6500 time to fit residues: 229.1066 Evaluate side-chains 341 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 228 SER 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 345 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 407 LEU 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 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 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 352 TYR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 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 292 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 403 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 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3767 r_free = 0.3767 target = 0.124600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112284 restraints weight = 15698.805| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.60 r_work: 0.3499 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12021 Z= 0.148 Angle : 0.537 7.983 16290 Z= 0.287 Chirality : 0.044 0.279 1770 Planarity : 0.004 0.044 2097 Dihedral : 5.321 57.727 1764 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 3.26 % Allowed : 28.91 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1452 helix: 2.50 (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 ARG 0.010 0.001 ARG C 192 TYR 0.025 0.001 TYR A 489 PHE 0.031 0.002 PHE C 339 TRP 0.010 0.001 TRP C 422 HIS 0.016 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00347 (11994) covalent geometry : angle 0.52837 (16227) SS BOND : bond 0.00460 ( 18) SS BOND : angle 1.30643 ( 36) hydrogen bonds : bond 0.05217 ( 462) hydrogen bonds : angle 4.75993 ( 1356) link_NAG-ASN : bond 0.00308 ( 9) link_NAG-ASN : angle 2.00701 ( 27) ********************** 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 345 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 341 GLU cc_start: 0.7286 (mp0) cc_final: 0.6975 (mp0) REVERT: A 345 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: A 458 ASP cc_start: 0.7930 (t0) cc_final: 0.7593 (t0) REVERT: B 186 ASN cc_start: 0.8481 (t0) cc_final: 0.8237 (OUTLIER) REVERT: B 436 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7368 (mtp180) REVERT: B 491 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7245 (mtpt) outliers start: 42 outliers final: 35 residues processed: 323 average time/residue: 0.6497 time to fit residues: 224.6853 Evaluate side-chains 339 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 478 CYS 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 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 352 TYR Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 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 292 THR Chi-restraints excluded: chain B residue 340 ILE 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 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 80 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 116 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 160 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 = 0.3771 r_free = 0.3771 target = 0.125031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113034 restraints weight = 15933.171| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.58 r_work: 0.3509 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12021 Z= 0.119 Angle : 0.525 8.141 16290 Z= 0.278 Chirality : 0.042 0.267 1770 Planarity : 0.004 0.039 2097 Dihedral : 5.183 58.062 1764 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.26 % Allowed : 29.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.22), residues: 1452 helix: 2.61 (0.27), residues: 378 sheet: 0.57 (0.32), residues: 303 loop : -1.19 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.028 0.001 TYR A 489 PHE 0.029 0.001 PHE C 339 TRP 0.010 0.001 TRP C 422 HIS 0.015 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00273 (11994) covalent geometry : angle 0.51765 (16227) SS BOND : bond 0.00398 ( 18) SS BOND : angle 1.24616 ( 36) hydrogen bonds : bond 0.04814 ( 462) hydrogen bonds : angle 4.65050 ( 1356) link_NAG-ASN : bond 0.00309 ( 9) link_NAG-ASN : angle 1.85744 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5617.25 seconds wall clock time: 96 minutes 11.34 seconds (5771.34 seconds total)