Starting phenix.real_space_refine on Sun May 3 11:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11mz_75853/05_2026/11mz_75853.cif Found real_map, /net/cci-nas-00/data/ceres_data/11mz_75853/05_2026/11mz_75853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11mz_75853/05_2026/11mz_75853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11mz_75853/05_2026/11mz_75853.map" model { file = "/net/cci-nas-00/data/ceres_data/11mz_75853/05_2026/11mz_75853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11mz_75853/05_2026/11mz_75853.cif" } resolution = 2.64 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= 0.000 sd= 0.006 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 51 5.16 5 C 7341 2.51 5 N 1998 2.21 5 O 3011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12401 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3880 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 20, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3880 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 20, 'TRANS': 469} Chain breaks: 1 Chain: "C" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3880 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 20, 'TRANS': 469} Chain breaks: 1 Chain: "A" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 257 Classifications: {'water': 257} Link IDs: {None: 256} Chain: "B" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 248 Classifications: {'water': 248} Link IDs: {None: 247} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 256 Classifications: {'water': 256} Link IDs: {None: 255} Time building chain proxies: 3.11, per 1000 atoms: 0.25 Number of scatterers: 12401 At special positions: 0 Unit cell: (85.26, 87.465, 147.735, 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 51 16.00 O 3011 8.00 N 1998 7.00 C 7341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.01 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 481 " distance=2.04 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 84 " distance=2.01 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 84 " distance=2.01 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 488 " - pdb=" SG CYS C 492 " 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 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 581.9 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 28.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.711A pdb=" N GLU A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.509A pdb=" N TRP A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 382 through 402 Processing helix chain 'A' and resid 418 through 470 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 removed outlier: 4.060A pdb=" N TYR A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLU A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.753A pdb=" N GLU B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.594A pdb=" N TRP B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 418 through 470 Processing helix chain 'B' and resid 489 through 498 Processing helix chain 'B' and resid 502 through 516 removed outlier: 4.058A pdb=" N TYR B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.776A pdb=" N GLU C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.509A pdb=" N TRP C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 381 through 402 removed outlier: 3.620A pdb=" N THR C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 469 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.976A pdb=" N TYR C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU C 509 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.716A pdb=" N GLY A 23 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.146A pdb=" N ASP A 31 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 removed outlier: 5.630A pdb=" N LEU A 58 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N CYS A 292 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.516A pdb=" N LEU A 67 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE A 96 " --> pdb=" O ILE A 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.805A pdb=" N SER A 127 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU A 193 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.805A pdb=" N SER A 127 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 150 through 155 removed outlier: 4.712A pdb=" N CYS A 153 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 178 through 183 Processing sheet with id=AB2, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.898A pdb=" N CYS A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 408 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 377 through 379 Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.117A pdb=" N ASP B 31 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AB6, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'B' and resid 58 through 61 removed outlier: 5.584A pdb=" N LEU B 58 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N CYS B 292 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 67 through 69 removed outlier: 6.539A pdb=" N LEU B 67 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 96 " --> pdb=" O ILE B 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 125 through 131 removed outlier: 3.793A pdb=" N SER B 127 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU B 193 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 125 through 131 removed outlier: 3.793A pdb=" N SER B 127 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 150 through 155 removed outlier: 4.712A pdb=" N CYS B 153 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AC4, first strand: chain 'B' and resid 302 through 303 removed outlier: 3.899A pdb=" N CYS B 296 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 408 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 377 through 380 Processing sheet with id=AC6, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.117A pdb=" N ASP C 31 " --> pdb=" O VAL C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AC8, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AC9, first strand: chain 'C' and resid 58 through 61 removed outlier: 5.625A pdb=" N LEU C 58 " --> pdb=" O HIS C 290 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N CYS C 292 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 67 through 69 removed outlier: 6.530A pdb=" N LEU C 67 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 96 " --> pdb=" O ILE C 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.801A pdb=" N SER C 127 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR C 270 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU C 193 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 189 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU C 193 " --> pdb=" O PRO C 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.801A pdb=" N SER C 127 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR C 270 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU C 193 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 189 " --> pdb=" O MET C 274 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 150 through 155 removed outlier: 4.715A pdb=" N CYS C 153 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 178 through 183 Processing sheet with id=AD6, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.898A pdb=" N CYS C 296 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 408 " --> pdb=" O GLY C 318 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3664 1.34 - 1.46: 1986 1.46 - 1.57: 6197 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11913 Sorted by residual: bond pdb=" N ILE B 282 " pdb=" CA ILE B 282 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.14e-02 7.69e+03 1.62e+01 bond pdb=" N GLN C 210 " pdb=" CA GLN C 210 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" N ILE B 283 " pdb=" CA ILE B 283 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.17e-02 7.31e+03 1.20e+01 bond pdb=" N THR C 298 " pdb=" CA THR C 298 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.11e-02 8.12e+03 9.78e+00 bond pdb=" N ASN C 473 " pdb=" CA ASN C 473 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.52e+00 ... (remaining 11908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 15283 1.58 - 3.16: 741 3.16 - 4.74: 98 4.74 - 6.32: 9 6.32 - 7.91: 9 Bond angle restraints: 16140 Sorted by residual: angle pdb=" N GLY C 367 " pdb=" CA GLY C 367 " pdb=" C GLY C 367 " ideal model delta sigma weight residual 111.08 118.98 -7.90 1.62e+00 3.81e-01 2.38e+01 angle pdb=" N LYS C 471 " pdb=" CA LYS C 471 " pdb=" C LYS C 471 " ideal model delta sigma weight residual 111.28 106.17 5.11 1.09e+00 8.42e-01 2.20e+01 angle pdb=" N LYS C 188 " pdb=" CA LYS C 188 " pdb=" C LYS C 188 " ideal model delta sigma weight residual 109.52 116.70 -7.18 1.55e+00 4.16e-01 2.15e+01 angle pdb=" N ALA B 278 " pdb=" CA ALA B 278 " pdb=" C ALA B 278 " ideal model delta sigma weight residual 110.50 116.70 -6.20 1.41e+00 5.03e-01 1.93e+01 angle pdb=" N SER B 280 " pdb=" CA SER B 280 " pdb=" C SER B 280 " ideal model delta sigma weight residual 111.28 115.89 -4.61 1.09e+00 8.42e-01 1.79e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 6497 17.49 - 34.98: 474 34.98 - 52.48: 113 52.48 - 69.97: 38 69.97 - 87.46: 18 Dihedral angle restraints: 7140 sinusoidal: 2877 harmonic: 4263 Sorted by residual: dihedral pdb=" CA ALA C 278 " pdb=" C ALA C 278 " pdb=" N GLY C 279 " pdb=" CA GLY C 279 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ALA A 278 " pdb=" C ALA A 278 " pdb=" N GLY A 279 " pdb=" CA GLY A 279 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG C 514 " pdb=" CD ARG C 514 " pdb=" NE ARG C 514 " pdb=" CZ ARG C 514 " ideal model delta sinusoidal sigma weight residual 180.00 136.03 43.97 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 7137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1201 0.045 - 0.089: 353 0.089 - 0.134: 145 0.134 - 0.179: 35 0.179 - 0.224: 9 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CB VAL C 216 " pdb=" CA VAL C 216 " pdb=" CG1 VAL C 216 " pdb=" CG2 VAL C 216 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA TYR B 485 " pdb=" N TYR B 485 " pdb=" C TYR B 485 " pdb=" CB TYR B 485 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA VAL C 216 " pdb=" N VAL C 216 " pdb=" C VAL C 216 " pdb=" CB VAL C 216 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1740 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 50 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C LEU A 50 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU A 50 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 51 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 226 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" C LYS A 226 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS A 226 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE A 227 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 470 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C LEU A 470 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 470 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 471 " -0.014 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2336 2.78 - 3.31: 11374 3.31 - 3.84: 21960 3.84 - 4.37: 27698 4.37 - 4.90: 45849 Nonbonded interactions: 109217 Sorted by model distance: nonbonded pdb=" O SER A 94 " pdb=" OG SER A 280 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR A 298 " pdb=" O GLY A 301 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 298 " pdb=" O GLY B 301 " model vdw 2.283 3.040 nonbonded pdb=" O SER C 92 " pdb=" O HOH C 601 " model vdw 2.303 3.040 nonbonded pdb=" OD2 ASP C 31 " pdb=" O HOH C 602 " model vdw 2.311 3.040 ... (remaining 109212 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.980 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.005 0.061 11928 Z= 0.330 Angle : 0.744 7.905 16170 Z= 0.488 Chirality : 0.052 0.224 1743 Planarity : 0.004 0.032 2088 Dihedral : 14.279 87.462 4365 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.01 % Allowed : 1.32 % Favored : 97.67 % 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 are not related in a simple way. whole: 0.20 (0.20), residues: 1458 helix: 1.83 (0.26), residues: 369 sheet: 0.19 (0.30), residues: 288 loop : -0.70 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 276 TYR 0.012 0.002 TYR A 246 PHE 0.010 0.002 PHE B 484 TRP 0.007 0.001 TRP C 140 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.00510 (11913) covalent geometry : angle 0.74384 (16140) SS BOND : bond 0.00804 ( 15) SS BOND : angle 0.79334 ( 30) hydrogen bonds : bond 0.16321 ( 484) hydrogen bonds : angle 7.07009 ( 1419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.6757 (m-30) cc_final: 0.6296 (m-30) REVERT: A 53 LYS cc_start: 0.7579 (mppt) cc_final: 0.7004 (mtpm) REVERT: A 91 SER cc_start: 0.8304 (p) cc_final: 0.8053 (t) REVERT: A 121 GLN cc_start: 0.8761 (mm110) cc_final: 0.8522 (mm-40) REVERT: A 163 LYS cc_start: 0.8772 (mttt) cc_final: 0.8255 (mmpt) REVERT: A 252 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7555 (mp0) REVERT: A 275 GLU cc_start: 0.8034 (tt0) cc_final: 0.7698 (mt-10) REVERT: A 328 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7748 (ptmt) REVERT: A 426 LYS cc_start: 0.8340 (tttt) cc_final: 0.8029 (ttpp) REVERT: A 456 ASP cc_start: 0.8072 (m-30) cc_final: 0.7734 (m-30) REVERT: A 460 LYS cc_start: 0.6715 (ptpt) cc_final: 0.6453 (tmmt) REVERT: A 513 ASN cc_start: 0.6704 (m110) cc_final: 0.6482 (m110) REVERT: B 53 LYS cc_start: 0.7506 (mppt) cc_final: 0.6933 (mtpm) REVERT: B 62 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7267 (mtm180) REVERT: B 163 LYS cc_start: 0.8781 (mttt) cc_final: 0.8336 (mmpt) REVERT: B 204 ASP cc_start: 0.6817 (t0) cc_final: 0.6316 (m-30) REVERT: B 252 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7708 (mp0) REVERT: B 275 GLU cc_start: 0.8052 (tt0) cc_final: 0.7763 (mt-10) REVERT: B 292 CYS cc_start: 0.7137 (t) cc_final: 0.6271 (p) REVERT: B 363 ASP cc_start: 0.7734 (t0) cc_final: 0.7491 (t0) REVERT: B 387 ASN cc_start: 0.7616 (t0) cc_final: 0.7354 (t0) REVERT: B 426 LYS cc_start: 0.8434 (tttt) cc_final: 0.8104 (ttpp) REVERT: B 456 ASP cc_start: 0.7983 (m-30) cc_final: 0.7657 (m-30) REVERT: B 460 LYS cc_start: 0.6746 (ptpt) cc_final: 0.6510 (tmmt) REVERT: B 464 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6218 (mt-10) REVERT: B 471 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7355 (pttt) REVERT: C 53 LYS cc_start: 0.7728 (mppt) cc_final: 0.7255 (mtpm) REVERT: C 163 LYS cc_start: 0.8798 (mttt) cc_final: 0.8320 (mmpt) REVERT: C 173 ASN cc_start: 0.8323 (m-40) cc_final: 0.8094 (m-40) REVERT: C 252 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7048 (pt0) REVERT: C 275 GLU cc_start: 0.8036 (tt0) cc_final: 0.7671 (mt-10) REVERT: C 328 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7906 (ptmt) REVERT: C 456 ASP cc_start: 0.8088 (m-30) cc_final: 0.7780 (m-30) outliers start: 13 outliers final: 1 residues processed: 244 average time/residue: 0.6222 time to fit residues: 164.1599 Evaluate side-chains 152 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 471 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 210 GLN A 387 ASN A 394 ASN A 415 ASN B 245 ASN B 370 HIS B 394 ASN B 415 ASN B 469 GLN C 68 HIS C 210 GLN C 394 ASN C 415 ASN C 423 ASN C 513 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108020 restraints weight = 13359.796| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.68 r_work: 0.3164 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11928 Z= 0.248 Angle : 0.644 8.865 16170 Z= 0.343 Chirality : 0.048 0.174 1743 Planarity : 0.004 0.033 2088 Dihedral : 5.358 56.204 1584 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.18 % Allowed : 6.92 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1458 helix: 2.03 (0.26), residues: 375 sheet: 0.04 (0.29), residues: 321 loop : -0.82 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 243 TYR 0.016 0.002 TYR C 246 PHE 0.021 0.002 PHE C 482 TRP 0.007 0.001 TRP A 365 HIS 0.007 0.002 HIS C 25 Details of bonding type rmsd covalent geometry : bond 0.00608 (11913) covalent geometry : angle 0.64074 (16140) SS BOND : bond 0.00661 ( 15) SS BOND : angle 1.57330 ( 30) hydrogen bonds : bond 0.05652 ( 484) hydrogen bonds : angle 5.53031 ( 1419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7714 (mppt) cc_final: 0.6890 (mtpm) REVERT: A 62 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.7096 (mtm180) REVERT: A 188 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8530 (pttt) REVERT: A 204 ASP cc_start: 0.7129 (t0) cc_final: 0.6340 (m-30) REVERT: A 252 GLU cc_start: 0.7894 (mm-30) cc_final: 0.6630 (pm20) REVERT: A 290 HIS cc_start: 0.7418 (t70) cc_final: 0.6002 (m90) REVERT: A 292 CYS cc_start: 0.7356 (t) cc_final: 0.6337 (p) REVERT: A 328 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7569 (ptmt) REVERT: A 426 LYS cc_start: 0.8018 (tttt) cc_final: 0.7704 (ttpt) REVERT: A 456 ASP cc_start: 0.7991 (m-30) cc_final: 0.7603 (m-30) REVERT: A 460 LYS cc_start: 0.6739 (ptpt) cc_final: 0.6358 (tttm) REVERT: A 472 ASN cc_start: 0.7630 (m-40) cc_final: 0.7340 (m110) REVERT: A 492 CYS cc_start: 0.6692 (t) cc_final: 0.6400 (t) REVERT: B 53 LYS cc_start: 0.7751 (mppt) cc_final: 0.7050 (mtpm) REVERT: B 62 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7172 (mtm180) REVERT: B 163 LYS cc_start: 0.8767 (mttt) cc_final: 0.8081 (mmpt) REVERT: B 204 ASP cc_start: 0.7060 (t0) cc_final: 0.6294 (m-30) REVERT: B 252 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7594 (mp0) REVERT: B 275 GLU cc_start: 0.7772 (tt0) cc_final: 0.7389 (mt-10) REVERT: B 290 HIS cc_start: 0.7550 (t70) cc_final: 0.6204 (m90) REVERT: B 292 CYS cc_start: 0.7258 (t) cc_final: 0.6265 (p) REVERT: B 387 ASN cc_start: 0.7526 (t0) cc_final: 0.7169 (t0) REVERT: B 426 LYS cc_start: 0.8014 (tttt) cc_final: 0.7552 (ttpp) REVERT: B 456 ASP cc_start: 0.7908 (m-30) cc_final: 0.7507 (m-30) REVERT: B 460 LYS cc_start: 0.6754 (ptpt) cc_final: 0.6303 (tmmt) REVERT: B 464 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6180 (mt-10) REVERT: B 471 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7206 (pttt) REVERT: B 492 CYS cc_start: 0.6624 (t) cc_final: 0.6345 (t) REVERT: C 53 LYS cc_start: 0.7847 (mppt) cc_final: 0.7170 (mtpm) REVERT: C 62 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.7147 (mtm180) REVERT: C 163 LYS cc_start: 0.8707 (mttt) cc_final: 0.8039 (mmpt) REVERT: C 173 ASN cc_start: 0.8228 (m-40) cc_final: 0.7952 (m-40) REVERT: C 204 ASP cc_start: 0.7156 (t0) cc_final: 0.6299 (m-30) REVERT: C 239 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7910 (t0) REVERT: C 252 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7512 (mp0) REVERT: C 290 HIS cc_start: 0.7359 (t70) cc_final: 0.6054 (m90) REVERT: C 292 CYS cc_start: 0.7274 (t) cc_final: 0.6240 (p) REVERT: C 328 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7632 (ptmt) REVERT: C 387 ASN cc_start: 0.7492 (t0) cc_final: 0.7228 (t0) REVERT: C 449 GLU cc_start: 0.7764 (tt0) cc_final: 0.7523 (tt0) REVERT: C 456 ASP cc_start: 0.8011 (m-30) cc_final: 0.7646 (m-30) REVERT: C 513 ASN cc_start: 0.7041 (m-40) cc_final: 0.6774 (m110) outliers start: 28 outliers final: 12 residues processed: 187 average time/residue: 0.6391 time to fit residues: 129.3635 Evaluate side-chains 163 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 415 ASN B 415 ASN C 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109080 restraints weight = 13540.718| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.70 r_work: 0.3182 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11928 Z= 0.168 Angle : 0.569 9.214 16170 Z= 0.302 Chirality : 0.045 0.216 1743 Planarity : 0.004 0.030 2088 Dihedral : 5.100 56.767 1584 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.86 % Allowed : 9.17 % Favored : 88.97 % 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 are not related in a simple way. whole: 0.31 (0.20), residues: 1458 helix: 2.20 (0.26), residues: 375 sheet: 0.22 (0.30), residues: 288 loop : -0.80 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 243 TYR 0.015 0.002 TYR C 503 PHE 0.016 0.002 PHE C 482 TRP 0.006 0.001 TRP B 93 HIS 0.012 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00408 (11913) covalent geometry : angle 0.56149 (16140) SS BOND : bond 0.00444 ( 15) SS BOND : angle 2.16114 ( 30) hydrogen bonds : bond 0.04982 ( 484) hydrogen bonds : angle 5.19507 ( 1419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7731 (mppt) cc_final: 0.6940 (mtpm) REVERT: A 120 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: A 163 LYS cc_start: 0.8736 (mttt) cc_final: 0.8347 (mtmt) REVERT: A 188 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8466 (pttt) REVERT: A 204 ASP cc_start: 0.7110 (t0) cc_final: 0.6273 (m-30) REVERT: A 252 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7545 (mp0) REVERT: A 290 HIS cc_start: 0.7360 (t70) cc_final: 0.5956 (m90) REVERT: A 292 CYS cc_start: 0.7292 (t) cc_final: 0.6363 (p) REVERT: A 328 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7595 (ptmt) REVERT: A 426 LYS cc_start: 0.7984 (tttt) cc_final: 0.7677 (ttpt) REVERT: A 456 ASP cc_start: 0.7873 (m-30) cc_final: 0.7599 (m-30) REVERT: A 460 LYS cc_start: 0.6600 (ptpt) cc_final: 0.6343 (tttp) REVERT: B 53 LYS cc_start: 0.7799 (mppt) cc_final: 0.7044 (mtpm) REVERT: B 62 ARG cc_start: 0.7410 (mtm-85) cc_final: 0.7162 (mtm180) REVERT: B 163 LYS cc_start: 0.8740 (mttt) cc_final: 0.8099 (mmpt) REVERT: B 204 ASP cc_start: 0.7097 (t0) cc_final: 0.6270 (m-30) REVERT: B 252 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7578 (mp0) REVERT: B 275 GLU cc_start: 0.7762 (tt0) cc_final: 0.7338 (mt-10) REVERT: B 290 HIS cc_start: 0.7540 (t70) cc_final: 0.6176 (m90) REVERT: B 292 CYS cc_start: 0.7165 (t) cc_final: 0.6242 (p) REVERT: B 387 ASN cc_start: 0.7507 (t0) cc_final: 0.7171 (t0) REVERT: B 426 LYS cc_start: 0.7960 (tttt) cc_final: 0.7499 (ttpp) REVERT: B 456 ASP cc_start: 0.7853 (m-30) cc_final: 0.7454 (m-30) REVERT: B 460 LYS cc_start: 0.6661 (ptpt) cc_final: 0.6372 (tmmt) REVERT: C 53 LYS cc_start: 0.7838 (mppt) cc_final: 0.7097 (mtpm) REVERT: C 163 LYS cc_start: 0.8690 (mttt) cc_final: 0.8120 (mmpt) REVERT: C 173 ASN cc_start: 0.8251 (m-40) cc_final: 0.7979 (m-40) REVERT: C 204 ASP cc_start: 0.7186 (t0) cc_final: 0.6284 (m-30) REVERT: C 225 LYS cc_start: 0.9033 (tttt) cc_final: 0.8818 (tttp) REVERT: C 239 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (t0) REVERT: C 252 GLU cc_start: 0.7866 (mm-30) cc_final: 0.6948 (pt0) REVERT: C 290 HIS cc_start: 0.7416 (t70) cc_final: 0.6089 (m90) REVERT: C 292 CYS cc_start: 0.7111 (t) cc_final: 0.6136 (p) REVERT: C 328 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7571 (ptmt) REVERT: C 387 ASN cc_start: 0.7405 (t0) cc_final: 0.7148 (t0) REVERT: C 401 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: C 456 ASP cc_start: 0.7928 (m-30) cc_final: 0.7585 (m-30) REVERT: C 460 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6747 (tmtt) outliers start: 24 outliers final: 11 residues processed: 175 average time/residue: 0.6209 time to fit residues: 117.7526 Evaluate side-chains 161 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 9 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN A 394 ASN B 394 ASN B 415 ASN B 472 ASN C 370 HIS C 387 ASN C 394 ASN C 513 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108694 restraints weight = 13406.944| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.68 r_work: 0.3167 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11928 Z= 0.182 Angle : 0.570 8.774 16170 Z= 0.303 Chirality : 0.045 0.230 1743 Planarity : 0.004 0.030 2088 Dihedral : 4.889 59.272 1580 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.49 % Allowed : 10.80 % Favored : 86.71 % 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 are not related in a simple way. whole: 0.29 (0.21), residues: 1458 helix: 2.18 (0.26), residues: 375 sheet: 0.20 (0.31), residues: 288 loop : -0.81 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 243 TYR 0.013 0.002 TYR C 503 PHE 0.018 0.002 PHE C 482 TRP 0.006 0.001 TRP B 93 HIS 0.013 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00446 (11913) covalent geometry : angle 0.56118 (16140) SS BOND : bond 0.00581 ( 15) SS BOND : angle 2.39804 ( 30) hydrogen bonds : bond 0.04997 ( 484) hydrogen bonds : angle 5.17857 ( 1419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7856 (mppt) cc_final: 0.7039 (mtpm) REVERT: A 120 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: A 163 LYS cc_start: 0.8774 (mttt) cc_final: 0.8321 (mtmt) REVERT: A 188 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8501 (pttt) REVERT: A 204 ASP cc_start: 0.7162 (t0) cc_final: 0.6357 (m-30) REVERT: A 252 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7602 (mp0) REVERT: A 290 HIS cc_start: 0.7375 (t70) cc_final: 0.6003 (m90) REVERT: A 292 CYS cc_start: 0.7326 (t) cc_final: 0.6417 (p) REVERT: A 328 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7617 (ptmt) REVERT: A 401 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: A 426 LYS cc_start: 0.8050 (tttt) cc_final: 0.7760 (ttpt) REVERT: A 456 ASP cc_start: 0.7965 (m-30) cc_final: 0.7596 (m-30) REVERT: A 460 LYS cc_start: 0.6684 (ptpt) cc_final: 0.6423 (tttp) REVERT: B 53 LYS cc_start: 0.7899 (mppt) cc_final: 0.7149 (mtpm) REVERT: B 62 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7189 (mtm180) REVERT: B 130 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8775 (ttt180) REVERT: B 163 LYS cc_start: 0.8763 (mttt) cc_final: 0.8233 (mmpt) REVERT: B 204 ASP cc_start: 0.7115 (t0) cc_final: 0.6316 (m-30) REVERT: B 222 ARG cc_start: 0.8364 (mtt180) cc_final: 0.7774 (mtp180) REVERT: B 252 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7147 (pt0) REVERT: B 275 GLU cc_start: 0.7809 (tt0) cc_final: 0.7416 (mt-10) REVERT: B 290 HIS cc_start: 0.7568 (t70) cc_final: 0.6218 (m90) REVERT: B 292 CYS cc_start: 0.7161 (t) cc_final: 0.6296 (p) REVERT: B 387 ASN cc_start: 0.7569 (t0) cc_final: 0.7253 (t0) REVERT: B 401 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: B 426 LYS cc_start: 0.8023 (tttt) cc_final: 0.7581 (ttpp) REVERT: B 456 ASP cc_start: 0.7866 (m-30) cc_final: 0.7481 (m-30) REVERT: B 460 LYS cc_start: 0.6736 (ptpt) cc_final: 0.6169 (tmmt) REVERT: B 464 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6103 (mt-10) REVERT: C 34 ASP cc_start: 0.8213 (m-30) cc_final: 0.7985 (m-30) REVERT: C 53 LYS cc_start: 0.7919 (mppt) cc_final: 0.7162 (mtpm) REVERT: C 163 LYS cc_start: 0.8686 (mttt) cc_final: 0.8163 (mmpt) REVERT: C 173 ASN cc_start: 0.8283 (m-40) cc_final: 0.8029 (m-40) REVERT: C 204 ASP cc_start: 0.7222 (t0) cc_final: 0.6360 (m-30) REVERT: C 225 LYS cc_start: 0.9039 (tttt) cc_final: 0.8814 (tttm) REVERT: C 239 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7914 (t0) REVERT: C 252 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7063 (pt0) REVERT: C 290 HIS cc_start: 0.7407 (t70) cc_final: 0.6082 (m90) REVERT: C 292 CYS cc_start: 0.7146 (t) cc_final: 0.6200 (p) REVERT: C 328 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7634 (ptmt) REVERT: C 401 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: C 456 ASP cc_start: 0.7964 (m-30) cc_final: 0.7615 (m-30) REVERT: C 513 ASN cc_start: 0.6998 (m-40) cc_final: 0.6756 (m110) outliers start: 32 outliers final: 14 residues processed: 174 average time/residue: 0.6497 time to fit residues: 122.1211 Evaluate side-chains 165 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 206 GLN B 394 ASN B 415 ASN C 387 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109476 restraints weight = 13430.658| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.72 r_work: 0.3183 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11928 Z= 0.153 Angle : 0.543 9.471 16170 Z= 0.287 Chirality : 0.044 0.236 1743 Planarity : 0.004 0.029 2088 Dihedral : 4.745 55.710 1580 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.25 % Allowed : 12.20 % Favored : 85.55 % 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 are not related in a simple way. whole: 0.37 (0.21), residues: 1458 helix: 2.25 (0.26), residues: 375 sheet: 0.30 (0.31), residues: 288 loop : -0.78 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.012 0.001 TYR C 503 PHE 0.019 0.001 PHE C 482 TRP 0.006 0.001 TRP B 93 HIS 0.012 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00371 (11913) covalent geometry : angle 0.53224 (16140) SS BOND : bond 0.00643 ( 15) SS BOND : angle 2.52546 ( 30) hydrogen bonds : bond 0.04714 ( 484) hydrogen bonds : angle 5.03470 ( 1419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7860 (mppt) cc_final: 0.6985 (mtpm) REVERT: A 120 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: A 163 LYS cc_start: 0.8718 (mttt) cc_final: 0.8263 (mtmt) REVERT: A 188 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8415 (pttt) REVERT: A 204 ASP cc_start: 0.7088 (t0) cc_final: 0.6216 (m-30) REVERT: A 252 GLU cc_start: 0.7883 (mm-30) cc_final: 0.6951 (pt0) REVERT: A 290 HIS cc_start: 0.7343 (t70) cc_final: 0.5909 (m90) REVERT: A 292 CYS cc_start: 0.7218 (t) cc_final: 0.6280 (p) REVERT: A 328 LYS cc_start: 0.7874 (ttmt) cc_final: 0.7537 (ptmt) REVERT: A 401 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: A 426 LYS cc_start: 0.7905 (tttt) cc_final: 0.7540 (ttpt) REVERT: A 456 ASP cc_start: 0.7852 (m-30) cc_final: 0.7589 (m-30) REVERT: A 460 LYS cc_start: 0.6500 (ptpt) cc_final: 0.6261 (tttp) REVERT: B 25 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7800 (t-90) REVERT: B 53 LYS cc_start: 0.7886 (mppt) cc_final: 0.7085 (mtpm) REVERT: B 85 GLU cc_start: 0.7087 (pt0) cc_final: 0.6754 (mt-10) REVERT: B 130 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8758 (ttt180) REVERT: B 147 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7797 (mtpt) REVERT: B 163 LYS cc_start: 0.8692 (mttt) cc_final: 0.8350 (mmpt) REVERT: B 204 ASP cc_start: 0.7032 (t0) cc_final: 0.6170 (m-30) REVERT: B 222 ARG cc_start: 0.8339 (mtt180) cc_final: 0.7657 (mtp180) REVERT: B 252 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7034 (pt0) REVERT: B 275 GLU cc_start: 0.7692 (tt0) cc_final: 0.7279 (mt-10) REVERT: B 290 HIS cc_start: 0.7508 (t70) cc_final: 0.6073 (m90) REVERT: B 292 CYS cc_start: 0.7104 (t) cc_final: 0.6212 (p) REVERT: B 387 ASN cc_start: 0.7471 (t0) cc_final: 0.7150 (t0) REVERT: B 426 LYS cc_start: 0.7850 (tttt) cc_final: 0.7393 (ttpp) REVERT: B 456 ASP cc_start: 0.7789 (m-30) cc_final: 0.7388 (m-30) REVERT: B 460 LYS cc_start: 0.6594 (ptpt) cc_final: 0.6046 (tmmt) REVERT: B 464 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5789 (mt-10) REVERT: C 34 ASP cc_start: 0.8157 (m-30) cc_final: 0.7929 (m-30) REVERT: C 53 LYS cc_start: 0.7891 (mppt) cc_final: 0.7074 (mtpm) REVERT: C 85 GLU cc_start: 0.7206 (pt0) cc_final: 0.6952 (mt-10) REVERT: C 163 LYS cc_start: 0.8650 (mttt) cc_final: 0.8277 (mmpt) REVERT: C 173 ASN cc_start: 0.8254 (m-40) cc_final: 0.7988 (m-40) REVERT: C 204 ASP cc_start: 0.7178 (t0) cc_final: 0.6215 (m-30) REVERT: C 225 LYS cc_start: 0.8995 (tttt) cc_final: 0.8767 (tttm) REVERT: C 239 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7871 (t0) REVERT: C 252 GLU cc_start: 0.7882 (mm-30) cc_final: 0.6919 (pt0) REVERT: C 290 HIS cc_start: 0.7306 (t70) cc_final: 0.5982 (m90) REVERT: C 292 CYS cc_start: 0.7092 (t) cc_final: 0.6083 (p) REVERT: C 328 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7535 (ptmt) REVERT: C 401 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: C 426 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7243 (ttpp) REVERT: C 456 ASP cc_start: 0.7844 (m-30) cc_final: 0.7498 (m-30) outliers start: 29 outliers final: 13 residues processed: 176 average time/residue: 0.6570 time to fit residues: 124.7364 Evaluate side-chains 170 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.0040 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 394 ASN B 415 ASN C 387 ASN C 394 ASN C 513 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109412 restraints weight = 13419.618| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.67 r_work: 0.3183 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 11928 Z= 0.159 Angle : 0.559 11.058 16170 Z= 0.295 Chirality : 0.044 0.236 1743 Planarity : 0.004 0.040 2088 Dihedral : 4.678 44.285 1580 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.80 % Allowed : 12.28 % Favored : 84.93 % 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 are not related in a simple way. whole: 0.32 (0.21), residues: 1458 helix: 2.14 (0.26), residues: 375 sheet: 0.28 (0.31), residues: 288 loop : -0.78 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.013 0.001 TYR C 503 PHE 0.021 0.001 PHE C 482 TRP 0.006 0.001 TRP B 93 HIS 0.011 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00388 (11913) covalent geometry : angle 0.54555 (16140) SS BOND : bond 0.00760 ( 15) SS BOND : angle 2.84214 ( 30) hydrogen bonds : bond 0.04765 ( 484) hydrogen bonds : angle 5.04161 ( 1419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7957 (mppt) cc_final: 0.7120 (mtpm) REVERT: A 163 LYS cc_start: 0.8715 (mttt) cc_final: 0.8309 (mtmt) REVERT: A 188 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8485 (pttt) REVERT: A 204 ASP cc_start: 0.7157 (t0) cc_final: 0.6358 (m-30) REVERT: A 252 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7626 (mp0) REVERT: A 290 HIS cc_start: 0.7404 (t70) cc_final: 0.6003 (m90) REVERT: A 292 CYS cc_start: 0.7287 (t) cc_final: 0.6414 (p) REVERT: A 328 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7629 (ptmt) REVERT: A 401 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: A 426 LYS cc_start: 0.8065 (tttt) cc_final: 0.7733 (ttpt) REVERT: A 456 ASP cc_start: 0.7907 (m-30) cc_final: 0.7646 (m-30) REVERT: A 460 LYS cc_start: 0.6624 (ptpt) cc_final: 0.6392 (tttp) REVERT: B 53 LYS cc_start: 0.7990 (mppt) cc_final: 0.7235 (mtpm) REVERT: B 85 GLU cc_start: 0.7204 (pt0) cc_final: 0.6893 (mt-10) REVERT: B 130 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8777 (ttt180) REVERT: B 163 LYS cc_start: 0.8723 (mttt) cc_final: 0.8333 (mmpt) REVERT: B 204 ASP cc_start: 0.7080 (t0) cc_final: 0.6295 (m-30) REVERT: B 222 ARG cc_start: 0.8402 (mtt180) cc_final: 0.7764 (mtp180) REVERT: B 252 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7161 (pt0) REVERT: B 275 GLU cc_start: 0.7774 (tt0) cc_final: 0.7384 (mt-10) REVERT: B 290 HIS cc_start: 0.7546 (t70) cc_final: 0.6174 (m90) REVERT: B 292 CYS cc_start: 0.7093 (t) cc_final: 0.6250 (p) REVERT: B 387 ASN cc_start: 0.7564 (t0) cc_final: 0.7271 (t0) REVERT: B 401 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: B 426 LYS cc_start: 0.7997 (tttt) cc_final: 0.7506 (ttpp) REVERT: B 456 ASP cc_start: 0.7857 (m-30) cc_final: 0.7467 (m-30) REVERT: B 460 LYS cc_start: 0.6756 (ptpt) cc_final: 0.6229 (tmmt) REVERT: B 464 GLU cc_start: 0.6611 (mt-10) cc_final: 0.5938 (mt-10) REVERT: C 34 ASP cc_start: 0.8180 (m-30) cc_final: 0.7942 (m-30) REVERT: C 53 LYS cc_start: 0.7979 (mppt) cc_final: 0.7208 (mtpm) REVERT: C 85 GLU cc_start: 0.7334 (pt0) cc_final: 0.7063 (mt-10) REVERT: C 163 LYS cc_start: 0.8709 (mttt) cc_final: 0.8289 (mmpt) REVERT: C 173 ASN cc_start: 0.8277 (m-40) cc_final: 0.8026 (m-40) REVERT: C 204 ASP cc_start: 0.7250 (t0) cc_final: 0.6362 (m-30) REVERT: C 239 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7913 (t0) REVERT: C 252 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7060 (pt0) REVERT: C 290 HIS cc_start: 0.7353 (t70) cc_final: 0.6088 (m90) REVERT: C 292 CYS cc_start: 0.7116 (t) cc_final: 0.6194 (p) REVERT: C 328 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7633 (ptmt) REVERT: C 401 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: C 426 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7436 (ttpp) REVERT: C 456 ASP cc_start: 0.7887 (m-30) cc_final: 0.7540 (m-30) REVERT: C 513 ASN cc_start: 0.6905 (m-40) cc_final: 0.6696 (m110) outliers start: 36 outliers final: 19 residues processed: 166 average time/residue: 0.6297 time to fit residues: 113.1852 Evaluate side-chains 160 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 61 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111258 restraints weight = 13341.844| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.68 r_work: 0.3207 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11928 Z= 0.126 Angle : 0.531 12.264 16170 Z= 0.280 Chirality : 0.043 0.232 1743 Planarity : 0.004 0.029 2088 Dihedral : 4.350 19.530 1578 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.41 % Allowed : 13.21 % Favored : 84.38 % 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 are not related in a simple way. whole: 0.38 (0.21), residues: 1458 helix: 2.21 (0.26), residues: 375 sheet: 0.28 (0.31), residues: 288 loop : -0.73 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.011 0.001 TYR C 503 PHE 0.019 0.001 PHE C 482 TRP 0.006 0.001 TRP B 93 HIS 0.010 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00300 (11913) covalent geometry : angle 0.51678 (16140) SS BOND : bond 0.00712 ( 15) SS BOND : angle 2.88532 ( 30) hydrogen bonds : bond 0.04446 ( 484) hydrogen bonds : angle 4.90824 ( 1419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8027 (mppt) cc_final: 0.7198 (mtpm) REVERT: A 163 LYS cc_start: 0.8717 (mttt) cc_final: 0.8414 (mtmt) REVERT: A 188 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8458 (pttt) REVERT: A 204 ASP cc_start: 0.7142 (t0) cc_final: 0.6355 (m-30) REVERT: A 252 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7047 (pt0) REVERT: A 290 HIS cc_start: 0.7441 (t70) cc_final: 0.6091 (m90) REVERT: A 292 CYS cc_start: 0.7229 (t) cc_final: 0.6437 (p) REVERT: A 328 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7623 (ptmt) REVERT: A 401 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: A 426 LYS cc_start: 0.8092 (tttt) cc_final: 0.7692 (ttpp) REVERT: A 460 LYS cc_start: 0.6568 (ptpt) cc_final: 0.6359 (tttp) REVERT: B 53 LYS cc_start: 0.8031 (mppt) cc_final: 0.7245 (mtpm) REVERT: B 62 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6911 (mtm-85) REVERT: B 85 GLU cc_start: 0.7195 (pt0) cc_final: 0.6867 (mt-10) REVERT: B 130 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8762 (ttt180) REVERT: B 163 LYS cc_start: 0.8699 (mttt) cc_final: 0.8421 (mmpt) REVERT: B 204 ASP cc_start: 0.7071 (t0) cc_final: 0.6300 (m-30) REVERT: B 222 ARG cc_start: 0.8413 (mtt180) cc_final: 0.7773 (mtm110) REVERT: B 252 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7136 (pt0) REVERT: B 290 HIS cc_start: 0.7528 (t70) cc_final: 0.6180 (m90) REVERT: B 292 CYS cc_start: 0.7015 (t) cc_final: 0.6276 (p) REVERT: B 387 ASN cc_start: 0.7525 (t0) cc_final: 0.7270 (t0) REVERT: B 401 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: B 426 LYS cc_start: 0.8049 (tttt) cc_final: 0.7577 (ttpp) REVERT: B 456 ASP cc_start: 0.7849 (m-30) cc_final: 0.7453 (m-30) REVERT: B 460 LYS cc_start: 0.6701 (ptpt) cc_final: 0.6408 (tmtt) REVERT: C 34 ASP cc_start: 0.8152 (m-30) cc_final: 0.7905 (m-30) REVERT: C 53 LYS cc_start: 0.8002 (mppt) cc_final: 0.7216 (mtpm) REVERT: C 85 GLU cc_start: 0.7282 (pt0) cc_final: 0.7040 (mt-10) REVERT: C 163 LYS cc_start: 0.8666 (mttt) cc_final: 0.8293 (mmpt) REVERT: C 173 ASN cc_start: 0.8256 (m-40) cc_final: 0.8026 (m-40) REVERT: C 204 ASP cc_start: 0.7213 (t0) cc_final: 0.6334 (m-30) REVERT: C 239 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7833 (t0) REVERT: C 252 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7009 (pt0) REVERT: C 290 HIS cc_start: 0.7350 (t70) cc_final: 0.6128 (m90) REVERT: C 292 CYS cc_start: 0.7120 (t) cc_final: 0.6248 (p) REVERT: C 328 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7638 (ptmt) REVERT: C 426 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7475 (ttpp) REVERT: C 456 ASP cc_start: 0.7815 (m-30) cc_final: 0.7461 (m-30) outliers start: 31 outliers final: 16 residues processed: 167 average time/residue: 0.6286 time to fit residues: 114.1150 Evaluate side-chains 158 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN A 394 ASN A 423 ASN B 394 ASN B 415 ASN C 387 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110418 restraints weight = 13416.996| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.68 r_work: 0.3195 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11928 Z= 0.139 Angle : 0.555 14.292 16170 Z= 0.289 Chirality : 0.044 0.229 1743 Planarity : 0.004 0.044 2088 Dihedral : 4.417 20.406 1578 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.10 % Allowed : 13.99 % Favored : 83.92 % 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 are not related in a simple way. whole: 0.38 (0.21), residues: 1458 helix: 2.15 (0.26), residues: 375 sheet: 0.29 (0.33), residues: 273 loop : -0.68 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 450 TYR 0.011 0.001 TYR C 503 PHE 0.023 0.001 PHE C 482 TRP 0.005 0.001 TRP B 93 HIS 0.010 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00332 (11913) covalent geometry : angle 0.54546 (16140) SS BOND : bond 0.00756 ( 15) SS BOND : angle 2.39815 ( 30) hydrogen bonds : bond 0.04539 ( 484) hydrogen bonds : angle 4.94804 ( 1419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8039 (mppt) cc_final: 0.7199 (mtpm) REVERT: A 163 LYS cc_start: 0.8712 (mttt) cc_final: 0.8441 (mtmt) REVERT: A 188 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8474 (pttt) REVERT: A 204 ASP cc_start: 0.7186 (t0) cc_final: 0.6386 (m-30) REVERT: A 252 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7042 (pt0) REVERT: A 290 HIS cc_start: 0.7448 (t70) cc_final: 0.6093 (m90) REVERT: A 292 CYS cc_start: 0.7272 (t) cc_final: 0.6471 (p) REVERT: A 328 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7644 (ptmt) REVERT: A 401 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: A 426 LYS cc_start: 0.8093 (tttt) cc_final: 0.7686 (ttpp) REVERT: A 460 LYS cc_start: 0.6569 (ptpt) cc_final: 0.6358 (tttp) REVERT: B 53 LYS cc_start: 0.8036 (mppt) cc_final: 0.7240 (mtpm) REVERT: B 62 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6914 (mtm-85) REVERT: B 130 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8767 (ttt180) REVERT: B 163 LYS cc_start: 0.8688 (mttt) cc_final: 0.8312 (mmpt) REVERT: B 204 ASP cc_start: 0.7044 (t0) cc_final: 0.6281 (m-30) REVERT: B 222 ARG cc_start: 0.8413 (mtt180) cc_final: 0.7764 (mtm110) REVERT: B 252 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7155 (pt0) REVERT: B 290 HIS cc_start: 0.7513 (t70) cc_final: 0.6184 (m90) REVERT: B 292 CYS cc_start: 0.7043 (t) cc_final: 0.6275 (p) REVERT: B 387 ASN cc_start: 0.7565 (t0) cc_final: 0.7299 (t0) REVERT: B 401 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: B 426 LYS cc_start: 0.8048 (tttt) cc_final: 0.7573 (ttpp) REVERT: B 456 ASP cc_start: 0.7849 (m-30) cc_final: 0.7452 (m-30) REVERT: B 460 LYS cc_start: 0.6720 (ptpt) cc_final: 0.6222 (tmmt) REVERT: B 464 GLU cc_start: 0.6487 (mt-10) cc_final: 0.5905 (mt-10) REVERT: C 34 ASP cc_start: 0.8151 (m-30) cc_final: 0.7914 (m-30) REVERT: C 53 LYS cc_start: 0.8004 (mppt) cc_final: 0.7219 (mtpm) REVERT: C 163 LYS cc_start: 0.8697 (mttt) cc_final: 0.8219 (mmpt) REVERT: C 173 ASN cc_start: 0.8255 (m-40) cc_final: 0.8018 (m-40) REVERT: C 204 ASP cc_start: 0.7243 (t0) cc_final: 0.6357 (m-30) REVERT: C 239 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7859 (t0) REVERT: C 252 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7048 (pt0) REVERT: C 290 HIS cc_start: 0.7364 (t70) cc_final: 0.6120 (OUTLIER) REVERT: C 292 CYS cc_start: 0.7106 (t) cc_final: 0.6215 (p) REVERT: C 328 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7665 (ptmt) REVERT: C 401 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: C 426 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7464 (ttpp) REVERT: C 456 ASP cc_start: 0.7823 (m-30) cc_final: 0.7460 (m-30) REVERT: C 513 ASN cc_start: 0.7062 (m110) cc_final: 0.6861 (m110) outliers start: 27 outliers final: 18 residues processed: 155 average time/residue: 0.6679 time to fit residues: 111.7461 Evaluate side-chains 159 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 127 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN A 394 ASN B 415 ASN C 387 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110615 restraints weight = 13372.962| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.70 r_work: 0.3187 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11928 Z= 0.133 Angle : 0.569 15.696 16170 Z= 0.296 Chirality : 0.044 0.322 1743 Planarity : 0.004 0.045 2088 Dihedral : 4.413 20.864 1578 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.33 % Allowed : 13.75 % Favored : 83.92 % 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 are not related in a simple way. whole: 0.37 (0.21), residues: 1458 helix: 2.10 (0.26), residues: 375 sheet: 0.29 (0.33), residues: 273 loop : -0.67 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 450 TYR 0.011 0.001 TYR C 503 PHE 0.023 0.001 PHE C 482 TRP 0.005 0.001 TRP B 93 HIS 0.009 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00311 (11913) covalent geometry : angle 0.55307 (16140) SS BOND : bond 0.00751 ( 15) SS BOND : angle 3.11800 ( 30) hydrogen bonds : bond 0.04510 ( 484) hydrogen bonds : angle 4.92435 ( 1419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8012 (mppt) cc_final: 0.7145 (mtpm) REVERT: A 120 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: A 163 LYS cc_start: 0.8709 (mttt) cc_final: 0.8402 (mtmt) REVERT: A 188 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8434 (pttt) REVERT: A 204 ASP cc_start: 0.7158 (t0) cc_final: 0.6327 (m-30) REVERT: A 252 GLU cc_start: 0.7883 (mm-30) cc_final: 0.6998 (pt0) REVERT: A 290 HIS cc_start: 0.7416 (t70) cc_final: 0.6035 (m90) REVERT: A 292 CYS cc_start: 0.7252 (t) cc_final: 0.6413 (p) REVERT: A 328 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7598 (ptmt) REVERT: A 401 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: A 426 LYS cc_start: 0.8033 (tttt) cc_final: 0.7610 (ttpp) REVERT: A 460 LYS cc_start: 0.6436 (ptpt) cc_final: 0.6163 (tttp) REVERT: B 53 LYS cc_start: 0.8002 (mppt) cc_final: 0.7179 (mtpm) REVERT: B 62 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6903 (mtm-85) REVERT: B 85 GLU cc_start: 0.7071 (pt0) cc_final: 0.6840 (mt-10) REVERT: B 130 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8768 (ttt180) REVERT: B 163 LYS cc_start: 0.8646 (mttt) cc_final: 0.8378 (mmpt) REVERT: B 204 ASP cc_start: 0.7017 (t0) cc_final: 0.6203 (m-30) REVERT: B 222 ARG cc_start: 0.8410 (mtt180) cc_final: 0.7716 (mtm110) REVERT: B 252 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7098 (pt0) REVERT: B 290 HIS cc_start: 0.7493 (t70) cc_final: 0.6121 (m90) REVERT: B 292 CYS cc_start: 0.6989 (t) cc_final: 0.6182 (p) REVERT: B 387 ASN cc_start: 0.7511 (t0) cc_final: 0.7240 (t0) REVERT: B 401 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: B 426 LYS cc_start: 0.7971 (tttt) cc_final: 0.7483 (ttpp) REVERT: B 456 ASP cc_start: 0.7794 (m-30) cc_final: 0.7380 (m-30) REVERT: B 460 LYS cc_start: 0.6632 (ptpt) cc_final: 0.6135 (tmmt) REVERT: B 464 GLU cc_start: 0.6420 (mt-10) cc_final: 0.5844 (mt-10) REVERT: C 34 ASP cc_start: 0.8141 (m-30) cc_final: 0.7897 (m-30) REVERT: C 53 LYS cc_start: 0.7970 (mppt) cc_final: 0.7157 (mtpm) REVERT: C 163 LYS cc_start: 0.8665 (mttt) cc_final: 0.8177 (mmpt) REVERT: C 173 ASN cc_start: 0.8237 (m-40) cc_final: 0.7996 (m-40) REVERT: C 204 ASP cc_start: 0.7206 (t0) cc_final: 0.6271 (m-30) REVERT: C 239 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7828 (t0) REVERT: C 252 GLU cc_start: 0.7895 (mm-30) cc_final: 0.6954 (pt0) REVERT: C 290 HIS cc_start: 0.7340 (t70) cc_final: 0.6067 (m90) REVERT: C 292 CYS cc_start: 0.7052 (t) cc_final: 0.6124 (p) REVERT: C 328 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7616 (ptmt) REVERT: C 401 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: C 426 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7365 (ttpp) REVERT: C 456 ASP cc_start: 0.7788 (m-30) cc_final: 0.7419 (m-30) outliers start: 30 outliers final: 17 residues processed: 151 average time/residue: 0.6770 time to fit residues: 110.4155 Evaluate side-chains 156 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 1 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 143 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 ASN B 394 ASN B 415 ASN C 387 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108956 restraints weight = 13502.104| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.70 r_work: 0.3177 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11928 Z= 0.174 Angle : 0.645 15.393 16170 Z= 0.334 Chirality : 0.047 0.412 1743 Planarity : 0.004 0.035 2088 Dihedral : 4.605 22.166 1578 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.18 % Allowed : 14.06 % Favored : 83.76 % 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 are not related in a simple way. whole: 0.28 (0.21), residues: 1458 helix: 1.96 (0.26), residues: 375 sheet: 0.30 (0.33), residues: 273 loop : -0.71 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 450 TYR 0.013 0.002 TYR C 503 PHE 0.024 0.002 PHE C 482 TRP 0.005 0.001 TRP B 436 HIS 0.009 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00417 (11913) covalent geometry : angle 0.62162 (16140) SS BOND : bond 0.00921 ( 15) SS BOND : angle 4.04123 ( 30) hydrogen bonds : bond 0.04834 ( 484) hydrogen bonds : angle 5.05995 ( 1419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7993 (mppt) cc_final: 0.7117 (mtpm) REVERT: A 120 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: A 163 LYS cc_start: 0.8669 (mttt) cc_final: 0.8212 (mmmt) REVERT: A 188 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8465 (pttt) REVERT: A 204 ASP cc_start: 0.7195 (t0) cc_final: 0.6337 (m-30) REVERT: A 252 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7587 (mp0) REVERT: A 290 HIS cc_start: 0.7400 (t70) cc_final: 0.5958 (m90) REVERT: A 292 CYS cc_start: 0.7286 (t) cc_final: 0.6368 (p) REVERT: A 328 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7606 (ptmt) REVERT: A 401 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: A 426 LYS cc_start: 0.7989 (tttt) cc_final: 0.7627 (ttpt) REVERT: A 460 LYS cc_start: 0.6541 (ptpt) cc_final: 0.6299 (tttp) REVERT: B 53 LYS cc_start: 0.7978 (mppt) cc_final: 0.7176 (mtpm) REVERT: B 85 GLU cc_start: 0.7135 (pt0) cc_final: 0.6828 (mt-10) REVERT: B 130 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8780 (ttt180) REVERT: B 163 LYS cc_start: 0.8652 (mttt) cc_final: 0.8386 (mmpt) REVERT: B 204 ASP cc_start: 0.7058 (t0) cc_final: 0.6220 (m-30) REVERT: B 222 ARG cc_start: 0.8411 (mtt180) cc_final: 0.7686 (mtm110) REVERT: B 252 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7127 (pt0) REVERT: B 290 HIS cc_start: 0.7516 (t70) cc_final: 0.6129 (m90) REVERT: B 292 CYS cc_start: 0.7015 (t) cc_final: 0.6079 (p) REVERT: B 387 ASN cc_start: 0.7557 (t0) cc_final: 0.7270 (t0) REVERT: B 401 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7583 (mt-10) REVERT: B 426 LYS cc_start: 0.7967 (tttt) cc_final: 0.7455 (ttpp) REVERT: B 456 ASP cc_start: 0.7827 (m-30) cc_final: 0.7434 (m-30) REVERT: B 460 LYS cc_start: 0.6686 (ptpt) cc_final: 0.6168 (tmmt) REVERT: B 464 GLU cc_start: 0.6493 (mt-10) cc_final: 0.5927 (mt-10) REVERT: C 34 ASP cc_start: 0.8157 (m-30) cc_final: 0.7918 (m-30) REVERT: C 53 LYS cc_start: 0.8006 (mppt) cc_final: 0.7192 (mtpm) REVERT: C 163 LYS cc_start: 0.8652 (mttt) cc_final: 0.8173 (mmpt) REVERT: C 173 ASN cc_start: 0.8273 (m-40) cc_final: 0.8005 (m-40) REVERT: C 204 ASP cc_start: 0.7216 (t0) cc_final: 0.6300 (m-30) REVERT: C 239 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7910 (t0) REVERT: C 252 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7020 (pt0) REVERT: C 290 HIS cc_start: 0.7385 (t70) cc_final: 0.6087 (m90) REVERT: C 292 CYS cc_start: 0.7080 (t) cc_final: 0.6107 (p) REVERT: C 328 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7608 (ptmt) REVERT: C 401 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: C 426 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7347 (ttpp) REVERT: C 456 ASP cc_start: 0.7874 (m-30) cc_final: 0.7502 (m-30) REVERT: C 498 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7184 (m110) outliers start: 28 outliers final: 17 residues processed: 149 average time/residue: 0.6509 time to fit residues: 104.9937 Evaluate side-chains 156 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 498 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 92 optimal weight: 0.5980 chunk 102 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 206 GLN B 415 ASN C 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112592 restraints weight = 13318.871| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.69 r_work: 0.3228 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11928 Z= 0.110 Angle : 0.576 16.066 16170 Z= 0.299 Chirality : 0.044 0.299 1743 Planarity : 0.003 0.033 2088 Dihedral : 4.419 29.616 1578 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.71 % Allowed : 14.69 % Favored : 83.61 % 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 are not related in a simple way. whole: 0.40 (0.21), residues: 1458 helix: 2.12 (0.26), residues: 375 sheet: 0.30 (0.33), residues: 273 loop : -0.64 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 450 TYR 0.010 0.001 TYR C 503 PHE 0.021 0.001 PHE C 482 TRP 0.005 0.001 TRP B 93 HIS 0.009 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00243 (11913) covalent geometry : angle 0.54781 (16140) SS BOND : bond 0.00523 ( 15) SS BOND : angle 4.15634 ( 30) hydrogen bonds : bond 0.04259 ( 484) hydrogen bonds : angle 4.85177 ( 1419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4785.73 seconds wall clock time: 82 minutes 27.00 seconds (4947.00 seconds total)