Starting phenix.real_space_refine on Wed Feb 4 11:12:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4g_47509/02_2026/9e4g_47509.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4g_47509/02_2026/9e4g_47509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e4g_47509/02_2026/9e4g_47509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4g_47509/02_2026/9e4g_47509.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e4g_47509/02_2026/9e4g_47509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4g_47509/02_2026/9e4g_47509.map" } resolution = 2.8 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= 0.015 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 87 5.16 5 C 6406 2.51 5 N 1644 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10024 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3349 Classifications: {'peptide': 418} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3370 Classifications: {'peptide': 420} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 401} Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Time building chain proxies: 2.57, per 1000 atoms: 0.26 Number of scatterers: 10024 At special positions: 0 Unit cell: (93.129, 97.324, 136.757, 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 87 16.00 O 1887 8.00 N 1644 7.00 C 6406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.04 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " 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: 0.70 Conformation dependent library (CDL) restraints added in 505.8 milliseconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 41.0% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 40 through 70 removed outlier: 4.232A pdb=" N ALA A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.715A pdb=" N ALA A 130 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.642A pdb=" N ILE A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.768A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 457 removed outlier: 4.394A pdb=" N LEU A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 70 removed outlier: 3.582A pdb=" N CYS B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.567A pdb=" N ILE B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 removed outlier: 4.021A pdb=" N ASP B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.624A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 454 removed outlier: 3.686A pdb=" N LEU B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'C' and resid 43 through 70 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 removed outlier: 4.057A pdb=" N ASP C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.504A pdb=" N LYS C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.540A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 450 removed outlier: 3.731A pdb=" N GLY C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 80 removed outlier: 5.793A pdb=" N ASP A 223 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU A 169 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 80 removed outlier: 6.242A pdb=" N PHE A 269 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP A 409 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR A 271 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE A 411 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL A 273 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A 413 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS A 275 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 415 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU A 277 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR A 417 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG A 279 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR A 419 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 281 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 421 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 7.042A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 80 removed outlier: 6.581A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 80 removed outlier: 4.043A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLU B 277 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU B 415 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N ARG B 279 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N TYR B 417 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 12.639A pdb=" N ILE B 281 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N THR B 419 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 7.096A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 80 removed outlier: 6.150A pdb=" N PHE C 412 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASN C 216 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 11.404A pdb=" N VAL C 414 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 10.809A pdb=" N THR C 214 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 80 removed outlier: 4.222A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU C 277 " --> pdb=" O GLU C 413 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N LEU C 415 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG C 279 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N TYR C 417 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 12.810A pdb=" N ILE C 281 " --> pdb=" O TYR C 417 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N THR C 419 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 7.122A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3267 1.35 - 1.47: 2468 1.47 - 1.59: 4402 1.59 - 1.71: 0 1.71 - 1.83: 120 Bond restraints: 10257 Sorted by residual: bond pdb=" C HIS A 329 " pdb=" N MET A 330 " ideal model delta sigma weight residual 1.331 1.308 0.023 2.07e-02 2.33e+03 1.26e+00 bond pdb=" N GLY B 288 " pdb=" CA GLY B 288 " ideal model delta sigma weight residual 1.453 1.444 0.009 8.60e-03 1.35e+04 1.00e+00 bond pdb=" CA TYR A 191 " pdb=" C TYR A 191 " ideal model delta sigma weight residual 1.523 1.509 0.014 1.41e-02 5.03e+03 9.88e-01 bond pdb=" CA VAL A 103 " pdb=" CB VAL A 103 " ideal model delta sigma weight residual 1.533 1.542 -0.009 1.20e-02 6.94e+03 6.15e-01 bond pdb=" C GLU B 403 " pdb=" N ASN B 404 " ideal model delta sigma weight residual 1.332 1.322 0.011 1.40e-02 5.10e+03 5.95e-01 ... (remaining 10252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 13264 1.09 - 2.18: 508 2.18 - 3.26: 72 3.26 - 4.35: 18 4.35 - 5.44: 7 Bond angle restraints: 13869 Sorted by residual: angle pdb=" CA CYS A 172 " pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " ideal model delta sigma weight residual 114.40 119.84 -5.44 2.30e+00 1.89e-01 5.60e+00 angle pdb=" CA CYS C 172 " pdb=" CB CYS C 172 " pdb=" SG CYS C 172 " ideal model delta sigma weight residual 114.40 119.57 -5.17 2.30e+00 1.89e-01 5.05e+00 angle pdb=" CA CYS B 172 " pdb=" CB CYS B 172 " pdb=" SG CYS B 172 " ideal model delta sigma weight residual 114.40 119.44 -5.04 2.30e+00 1.89e-01 4.80e+00 angle pdb=" C ASN B 322 " pdb=" N CYS B 323 " pdb=" CA CYS B 323 " ideal model delta sigma weight residual 122.79 119.78 3.01 1.63e+00 3.76e-01 3.41e+00 angle pdb=" N VAL A 273 " pdb=" CA VAL A 273 " pdb=" C VAL A 273 " ideal model delta sigma weight residual 106.53 109.07 -2.54 1.41e+00 5.03e-01 3.25e+00 ... (remaining 13864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5679 17.46 - 34.92: 405 34.92 - 52.38: 97 52.38 - 69.85: 24 69.85 - 87.31: 8 Dihedral angle restraints: 6213 sinusoidal: 2556 harmonic: 3657 Sorted by residual: dihedral pdb=" CB CYS A 314 " pdb=" SG CYS A 314 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 54.79 38.21 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS B 323 " pdb=" SG CYS B 323 " pdb=" SG CYS B 345 " pdb=" CB CYS B 345 " ideal model delta sinusoidal sigma weight residual 93.00 58.53 34.47 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CA ASN A 416 " pdb=" C ASN A 416 " pdb=" N TYR A 417 " pdb=" CA TYR A 417 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 6210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 927 0.029 - 0.059: 415 0.059 - 0.088: 90 0.088 - 0.118: 50 0.118 - 0.147: 8 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1487 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 284 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO B 285 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 285 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 285 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 158 " 0.005 2.00e-02 2.50e+03 7.59e-03 1.15e+00 pdb=" CG TYR B 158 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 158 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 158 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 158 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 158 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.05e+00 pdb=" N PRO B 339 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.014 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 934 2.74 - 3.28: 10145 3.28 - 3.82: 17086 3.82 - 4.36: 21079 4.36 - 4.90: 36020 Nonbonded interactions: 85264 Sorted by model distance: nonbonded pdb=" OH TYR C 305 " pdb=" O GLU C 364 " model vdw 2.206 3.040 nonbonded pdb=" OE2 GLU C 321 " pdb=" OH TYR C 360 " model vdw 2.241 3.040 nonbonded pdb=" ND2 ASN B 96 " pdb=" O PHE B 98 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR A 282 " pdb=" O GLU B 79 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU A 321 " pdb=" OH TYR A 360 " model vdw 2.278 3.040 ... (remaining 85259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 452) selection = (chain 'B' and resid 40 through 452) 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.670 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: 0.010 Load rotamer database and sin/cos tables:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 : 0.002 0.023 10278 Z= 0.116 Angle : 0.507 5.442 13911 Z= 0.285 Chirality : 0.037 0.147 1490 Planarity : 0.002 0.029 1808 Dihedral : 13.476 87.308 3804 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.84 (0.25), residues: 1245 helix: 1.09 (0.26), residues: 411 sheet: -0.45 (0.30), residues: 283 loop : 0.96 (0.30), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.018 0.001 TYR B 158 PHE 0.015 0.001 PHE B 257 TRP 0.005 0.001 TRP B 287 HIS 0.005 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00232 (10257) covalent geometry : angle 0.50099 (13869) SS BOND : bond 0.00239 ( 21) SS BOND : angle 1.53819 ( 42) hydrogen bonds : bond 0.20996 ( 488) hydrogen bonds : angle 9.22554 ( 1446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.404 Fit side-chains REVERT: A 380 LYS cc_start: 0.8440 (tttp) cc_final: 0.7865 (ttmm) REVERT: A 384 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8772 (mtmt) REVERT: B 136 GLU cc_start: 0.9097 (tp30) cc_final: 0.8470 (tm-30) REVERT: B 295 MET cc_start: 0.5953 (ptt) cc_final: 0.5092 (ppp) REVERT: B 333 ASP cc_start: 0.8441 (p0) cc_final: 0.8225 (p0) REVERT: B 438 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8073 (mm-40) REVERT: C 59 CYS cc_start: 0.8070 (m) cc_final: 0.7601 (p) REVERT: C 133 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8763 (tppt) REVERT: C 185 LYS cc_start: 0.8586 (tptt) cc_final: 0.8354 (tmmt) REVERT: C 219 GLU cc_start: 0.8626 (tt0) cc_final: 0.8311 (tm-30) REVERT: C 432 LEU cc_start: 0.8367 (mt) cc_final: 0.8109 (pt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.6705 time to fit residues: 126.3354 Evaluate side-chains 101 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN C 216 ASN C 329 HIS C 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075918 restraints weight = 16639.382| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.61 r_work: 0.2937 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10278 Z= 0.157 Angle : 0.662 9.510 13911 Z= 0.341 Chirality : 0.042 0.193 1490 Planarity : 0.004 0.033 1808 Dihedral : 4.745 25.505 1365 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 8.51 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.84 (0.24), residues: 1245 helix: 1.26 (0.25), residues: 412 sheet: -0.52 (0.28), residues: 284 loop : 0.85 (0.29), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 145 TYR 0.017 0.001 TYR A 342 PHE 0.012 0.001 PHE B 257 TRP 0.033 0.001 TRP A 46 HIS 0.003 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00344 (10257) covalent geometry : angle 0.65159 (13869) SS BOND : bond 0.00494 ( 21) SS BOND : angle 2.25048 ( 42) hydrogen bonds : bond 0.04963 ( 488) hydrogen bonds : angle 6.63118 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.316 Fit side-chains REVERT: A 208 LYS cc_start: 0.8901 (mttt) cc_final: 0.8696 (mttp) REVERT: A 210 MET cc_start: 0.7984 (mpt) cc_final: 0.7727 (mpt) REVERT: A 380 LYS cc_start: 0.8308 (tttp) cc_final: 0.7721 (ttmm) REVERT: A 439 MET cc_start: 0.8925 (tmm) cc_final: 0.8627 (ttt) REVERT: B 74 VAL cc_start: 0.8833 (p) cc_final: 0.8616 (m) REVERT: B 133 LYS cc_start: 0.9080 (tptt) cc_final: 0.8795 (tmmm) REVERT: B 136 GLU cc_start: 0.9222 (tp30) cc_final: 0.8729 (tm-30) REVERT: B 295 MET cc_start: 0.6016 (ptt) cc_final: 0.5058 (ppp) REVERT: B 303 ASP cc_start: 0.8426 (p0) cc_final: 0.7632 (m-30) REVERT: B 333 ASP cc_start: 0.8725 (p0) cc_final: 0.8515 (p0) REVERT: B 358 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8923 (tp-100) REVERT: B 365 MET cc_start: 0.8955 (mmm) cc_final: 0.8490 (mmm) REVERT: B 378 MET cc_start: 0.8867 (ptp) cc_final: 0.8579 (ptm) REVERT: B 438 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8159 (mm-40) REVERT: C 59 CYS cc_start: 0.8025 (m) cc_final: 0.7509 (p) REVERT: C 129 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6768 (ttp) REVERT: C 185 LYS cc_start: 0.8765 (tptt) cc_final: 0.8479 (tmmt) REVERT: C 210 MET cc_start: 0.8284 (mmm) cc_final: 0.7988 (mmm) REVERT: C 219 GLU cc_start: 0.8633 (tt0) cc_final: 0.8272 (tm-30) REVERT: C 340 GLU cc_start: 0.8254 (pt0) cc_final: 0.7885 (pm20) REVERT: C 432 LEU cc_start: 0.8457 (mt) cc_final: 0.8090 (pp) outliers start: 21 outliers final: 8 residues processed: 127 average time/residue: 0.5720 time to fit residues: 78.1689 Evaluate side-chains 109 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 358 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.6980 chunk 73 optimal weight: 0.0010 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS C 66 GLN C 70 HIS C 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.099922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.072774 restraints weight = 16549.088| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.77 r_work: 0.2821 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10278 Z= 0.149 Angle : 0.608 9.476 13911 Z= 0.310 Chirality : 0.041 0.189 1490 Planarity : 0.003 0.028 1808 Dihedral : 4.757 32.023 1365 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.10 % Allowed : 11.07 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.85 (0.24), residues: 1245 helix: 1.40 (0.25), residues: 412 sheet: -0.59 (0.28), residues: 284 loop : 0.78 (0.29), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.024 0.001 TYR B 360 PHE 0.009 0.001 PHE A 442 TRP 0.021 0.001 TRP A 46 HIS 0.002 0.000 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00329 (10257) covalent geometry : angle 0.59797 (13869) SS BOND : bond 0.00545 ( 21) SS BOND : angle 2.07448 ( 42) hydrogen bonds : bond 0.04427 ( 488) hydrogen bonds : angle 6.05165 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.434 Fit side-chains REVERT: A 208 LYS cc_start: 0.8946 (mttt) cc_final: 0.8743 (mttp) REVERT: A 340 GLU cc_start: 0.8460 (tp30) cc_final: 0.8250 (mp0) REVERT: A 380 LYS cc_start: 0.8368 (tttp) cc_final: 0.7795 (ttmm) REVERT: B 133 LYS cc_start: 0.9111 (tptt) cc_final: 0.8849 (tmmm) REVERT: B 136 GLU cc_start: 0.9198 (tp30) cc_final: 0.8707 (tm-30) REVERT: B 295 MET cc_start: 0.6049 (ptt) cc_final: 0.5177 (ppp) REVERT: B 303 ASP cc_start: 0.8370 (p0) cc_final: 0.7685 (m-30) REVERT: B 333 ASP cc_start: 0.8784 (p0) cc_final: 0.8575 (p0) REVERT: B 423 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8777 (mtpp) REVERT: B 434 ASP cc_start: 0.8363 (t70) cc_final: 0.8046 (t70) REVERT: B 438 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8210 (mm-40) REVERT: B 439 MET cc_start: 0.7861 (mmp) cc_final: 0.7531 (pp-130) REVERT: C 59 CYS cc_start: 0.7999 (m) cc_final: 0.7504 (p) REVERT: C 66 GLN cc_start: 0.8490 (tp40) cc_final: 0.8236 (mm-40) REVERT: C 129 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6714 (ttp) REVERT: C 185 LYS cc_start: 0.8795 (tptt) cc_final: 0.8533 (tmmt) REVERT: C 219 GLU cc_start: 0.8772 (tt0) cc_final: 0.8306 (tm-30) REVERT: C 340 GLU cc_start: 0.8259 (pt0) cc_final: 0.7875 (pm20) REVERT: C 409 ASP cc_start: 0.8951 (t70) cc_final: 0.8735 (m-30) REVERT: C 432 LEU cc_start: 0.8423 (mt) cc_final: 0.8068 (pp) outliers start: 23 outliers final: 11 residues processed: 118 average time/residue: 0.5973 time to fit residues: 75.8972 Evaluate side-chains 108 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 HIS C 216 ASN C 358 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.071637 restraints weight = 16741.404| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.78 r_work: 0.2799 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10278 Z= 0.171 Angle : 0.605 9.761 13911 Z= 0.305 Chirality : 0.041 0.191 1490 Planarity : 0.003 0.029 1808 Dihedral : 4.703 27.347 1365 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.20 % Allowed : 11.80 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.90 (0.24), residues: 1245 helix: 1.63 (0.26), residues: 411 sheet: -0.70 (0.28), residues: 284 loop : 0.74 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 145 TYR 0.012 0.001 TYR B 417 PHE 0.017 0.001 PHE B 50 TRP 0.018 0.001 TRP A 46 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00389 (10257) covalent geometry : angle 0.59690 (13869) SS BOND : bond 0.00509 ( 21) SS BOND : angle 1.84914 ( 42) hydrogen bonds : bond 0.04048 ( 488) hydrogen bonds : angle 5.84217 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.449 Fit side-chains REVERT: A 145 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8371 (mpp80) REVERT: A 208 LYS cc_start: 0.8932 (mttt) cc_final: 0.8725 (mttp) REVERT: A 340 GLU cc_start: 0.8507 (tp30) cc_final: 0.8235 (mp0) REVERT: A 380 LYS cc_start: 0.8336 (tttp) cc_final: 0.7766 (ttmm) REVERT: A 439 MET cc_start: 0.8892 (tpp) cc_final: 0.8486 (ttt) REVERT: B 133 LYS cc_start: 0.9099 (tptt) cc_final: 0.8822 (tmmm) REVERT: B 136 GLU cc_start: 0.9209 (tp30) cc_final: 0.8765 (tm-30) REVERT: B 295 MET cc_start: 0.6030 (ptt) cc_final: 0.5140 (ppp) REVERT: B 303 ASP cc_start: 0.8407 (p0) cc_final: 0.7727 (m-30) REVERT: B 333 ASP cc_start: 0.8824 (p0) cc_final: 0.8514 (p0) REVERT: B 358 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8776 (tp-100) REVERT: B 423 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8727 (mtpp) REVERT: B 438 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8203 (mm-40) REVERT: B 439 MET cc_start: 0.7864 (mmp) cc_final: 0.7552 (pp-130) REVERT: C 56 VAL cc_start: 0.6865 (t) cc_final: 0.6583 (p) REVERT: C 59 CYS cc_start: 0.8032 (m) cc_final: 0.7520 (p) REVERT: C 129 MET cc_start: 0.7533 (ptm) cc_final: 0.6813 (ttp) REVERT: C 185 LYS cc_start: 0.8785 (tptt) cc_final: 0.8477 (tmmt) REVERT: C 340 GLU cc_start: 0.8264 (pt0) cc_final: 0.7854 (pm20) REVERT: C 358 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: C 409 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8729 (m-30) outliers start: 24 outliers final: 10 residues processed: 112 average time/residue: 0.5661 time to fit residues: 68.3872 Evaluate side-chains 107 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 358 GLN Chi-restraints excluded: chain C residue 409 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN C 216 ASN C 358 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075185 restraints weight = 16746.577| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.62 r_work: 0.2915 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10278 Z= 0.148 Angle : 0.612 14.006 13911 Z= 0.308 Chirality : 0.040 0.171 1490 Planarity : 0.003 0.026 1808 Dihedral : 4.731 25.300 1365 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.38 % Allowed : 12.81 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.98 (0.24), residues: 1245 helix: 1.74 (0.26), residues: 411 sheet: -0.63 (0.28), residues: 284 loop : 0.73 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 201 TYR 0.016 0.001 TYR B 456 PHE 0.010 0.001 PHE A 442 TRP 0.017 0.001 TRP A 46 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00335 (10257) covalent geometry : angle 0.59840 (13869) SS BOND : bond 0.00518 ( 21) SS BOND : angle 2.43432 ( 42) hydrogen bonds : bond 0.03909 ( 488) hydrogen bonds : angle 5.70888 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.372 Fit side-chains REVERT: A 208 LYS cc_start: 0.8930 (mttt) cc_final: 0.8720 (mttp) REVERT: A 298 ASP cc_start: 0.8370 (p0) cc_final: 0.8145 (p0) REVERT: A 340 GLU cc_start: 0.8491 (tp30) cc_final: 0.8218 (mp0) REVERT: A 380 LYS cc_start: 0.8362 (tttp) cc_final: 0.7800 (ttmm) REVERT: B 136 GLU cc_start: 0.9159 (tp30) cc_final: 0.8738 (tm-30) REVERT: B 295 MET cc_start: 0.5992 (ptt) cc_final: 0.5132 (ppp) REVERT: B 303 ASP cc_start: 0.8439 (p0) cc_final: 0.7784 (m-30) REVERT: B 323 CYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6172 (t) REVERT: B 333 ASP cc_start: 0.8787 (p0) cc_final: 0.8475 (p0) REVERT: B 423 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8742 (mtpp) REVERT: B 438 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8139 (mm-40) REVERT: B 439 MET cc_start: 0.7877 (mmp) cc_final: 0.7610 (pp-130) REVERT: C 56 VAL cc_start: 0.6835 (t) cc_final: 0.6588 (p) REVERT: C 59 CYS cc_start: 0.8038 (m) cc_final: 0.7517 (p) REVERT: C 129 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6832 (ttp) REVERT: C 185 LYS cc_start: 0.8796 (tptt) cc_final: 0.8503 (tmmt) REVERT: C 210 MET cc_start: 0.8143 (mmm) cc_final: 0.7932 (mmm) REVERT: C 340 GLU cc_start: 0.8220 (pt0) cc_final: 0.7840 (pm20) REVERT: C 432 LEU cc_start: 0.8400 (mm) cc_final: 0.7828 (pp) outliers start: 26 outliers final: 9 residues processed: 113 average time/residue: 0.5837 time to fit residues: 71.0587 Evaluate side-chains 107 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.074848 restraints weight = 16707.257| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.63 r_work: 0.2912 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10278 Z= 0.163 Angle : 0.641 19.907 13911 Z= 0.313 Chirality : 0.041 0.172 1490 Planarity : 0.003 0.026 1808 Dihedral : 4.704 25.741 1365 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.20 % Allowed : 13.45 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.96 (0.24), residues: 1245 helix: 1.66 (0.26), residues: 416 sheet: -0.62 (0.28), residues: 283 loop : 0.75 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 201 TYR 0.012 0.001 TYR B 417 PHE 0.008 0.001 PHE B 454 TRP 0.017 0.001 TRP A 46 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00372 (10257) covalent geometry : angle 0.62904 (13869) SS BOND : bond 0.00432 ( 21) SS BOND : angle 2.33777 ( 42) hydrogen bonds : bond 0.03849 ( 488) hydrogen bonds : angle 5.60781 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.448 Fit side-chains REVERT: A 145 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8386 (mpp80) REVERT: A 298 ASP cc_start: 0.8339 (p0) cc_final: 0.8133 (p0) REVERT: A 340 GLU cc_start: 0.8515 (tp30) cc_final: 0.8215 (mp0) REVERT: A 365 MET cc_start: 0.8663 (mmm) cc_final: 0.8411 (ttp) REVERT: A 380 LYS cc_start: 0.8351 (tttp) cc_final: 0.7771 (ttmm) REVERT: A 439 MET cc_start: 0.8804 (tpp) cc_final: 0.8380 (ttp) REVERT: B 136 GLU cc_start: 0.9155 (tp30) cc_final: 0.8739 (tm-30) REVERT: B 201 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8058 (mmp-170) REVERT: B 295 MET cc_start: 0.6009 (ptt) cc_final: 0.5148 (ppp) REVERT: B 303 ASP cc_start: 0.8476 (p0) cc_final: 0.7851 (m-30) REVERT: B 323 CYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6387 (t) REVERT: B 333 ASP cc_start: 0.8803 (p0) cc_final: 0.8495 (p0) REVERT: B 359 GLU cc_start: 0.8781 (pt0) cc_final: 0.8346 (pp20) REVERT: B 423 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8730 (mtpp) REVERT: B 434 ASP cc_start: 0.8329 (t70) cc_final: 0.8019 (t70) REVERT: B 438 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8128 (mm-40) REVERT: B 439 MET cc_start: 0.7800 (mmp) cc_final: 0.7585 (pp-130) REVERT: C 129 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6892 (ttp) REVERT: C 185 LYS cc_start: 0.8779 (tptt) cc_final: 0.8477 (tmmt) REVERT: C 340 GLU cc_start: 0.8153 (pt0) cc_final: 0.7810 (pm20) REVERT: C 358 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7241 (mm110) REVERT: C 432 LEU cc_start: 0.8395 (mm) cc_final: 0.7814 (pp) REVERT: C 439 MET cc_start: 0.8927 (tpp) cc_final: 0.8713 (tpp) outliers start: 24 outliers final: 11 residues processed: 109 average time/residue: 0.6209 time to fit residues: 72.6901 Evaluate side-chains 107 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain C residue 69 PHE Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.072468 restraints weight = 16779.605| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.61 r_work: 0.2865 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10278 Z= 0.256 Angle : 0.668 11.142 13911 Z= 0.332 Chirality : 0.042 0.179 1490 Planarity : 0.003 0.027 1808 Dihedral : 4.878 26.595 1365 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.47 % Allowed : 14.18 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.90 (0.25), residues: 1245 helix: 1.73 (0.26), residues: 416 sheet: -0.77 (0.28), residues: 283 loop : 0.67 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 201 TYR 0.013 0.001 TYR A 342 PHE 0.015 0.001 PHE C 50 TRP 0.018 0.001 TRP A 46 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00595 (10257) covalent geometry : angle 0.65463 (13869) SS BOND : bond 0.00541 ( 21) SS BOND : angle 2.48215 ( 42) hydrogen bonds : bond 0.03874 ( 488) hydrogen bonds : angle 5.64499 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.404 Fit side-chains REVERT: A 145 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8457 (mpp80) REVERT: A 340 GLU cc_start: 0.8553 (tp30) cc_final: 0.8193 (mp0) REVERT: A 380 LYS cc_start: 0.8420 (tttp) cc_final: 0.7835 (ttmm) REVERT: B 72 HIS cc_start: 0.9116 (m90) cc_final: 0.8857 (m-70) REVERT: B 136 GLU cc_start: 0.9143 (tp30) cc_final: 0.8765 (tm-30) REVERT: B 295 MET cc_start: 0.6041 (ptt) cc_final: 0.5371 (ppp) REVERT: B 303 ASP cc_start: 0.8513 (p0) cc_final: 0.7858 (m-30) REVERT: B 333 ASP cc_start: 0.8786 (p0) cc_final: 0.8583 (p0) REVERT: B 423 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8756 (mtpp) REVERT: B 438 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8306 (mm-40) REVERT: B 439 MET cc_start: 0.7885 (mmp) cc_final: 0.7618 (pp-130) REVERT: C 59 CYS cc_start: 0.8089 (m) cc_final: 0.7418 (p) REVERT: C 129 MET cc_start: 0.7502 (ptm) cc_final: 0.7035 (ttp) REVERT: C 185 LYS cc_start: 0.8804 (tptt) cc_final: 0.8443 (tmmt) REVERT: C 340 GLU cc_start: 0.8176 (pt0) cc_final: 0.7832 (pm20) outliers start: 27 outliers final: 11 residues processed: 111 average time/residue: 0.5608 time to fit residues: 67.3703 Evaluate side-chains 99 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 450 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.073331 restraints weight = 16604.639| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.59 r_work: 0.2881 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10278 Z= 0.197 Angle : 0.665 13.155 13911 Z= 0.324 Chirality : 0.041 0.145 1490 Planarity : 0.003 0.026 1808 Dihedral : 4.850 27.022 1365 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.10 % Allowed : 14.91 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.81 (0.24), residues: 1245 helix: 1.65 (0.26), residues: 422 sheet: -0.82 (0.29), residues: 278 loop : 0.59 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 201 TYR 0.011 0.001 TYR B 417 PHE 0.015 0.001 PHE C 442 TRP 0.015 0.001 TRP A 46 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00457 (10257) covalent geometry : angle 0.65292 (13869) SS BOND : bond 0.00528 ( 21) SS BOND : angle 2.34352 ( 42) hydrogen bonds : bond 0.03806 ( 488) hydrogen bonds : angle 5.63133 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.421 Fit side-chains REVERT: A 145 ARG cc_start: 0.8793 (mmm160) cc_final: 0.8480 (mpp80) REVERT: A 340 GLU cc_start: 0.8539 (tp30) cc_final: 0.8193 (mp0) REVERT: A 380 LYS cc_start: 0.8404 (tttp) cc_final: 0.7811 (ttmm) REVERT: A 439 MET cc_start: 0.8756 (tpp) cc_final: 0.8378 (ttp) REVERT: B 72 HIS cc_start: 0.9113 (m90) cc_final: 0.8886 (m-70) REVERT: B 136 GLU cc_start: 0.9133 (tp30) cc_final: 0.8765 (tm-30) REVERT: B 201 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8206 (mmp-170) REVERT: B 295 MET cc_start: 0.6006 (ptt) cc_final: 0.5357 (ppp) REVERT: B 303 ASP cc_start: 0.8509 (p0) cc_final: 0.7901 (m-30) REVERT: B 321 GLU cc_start: 0.8967 (tt0) cc_final: 0.8734 (tt0) REVERT: B 333 ASP cc_start: 0.8805 (p0) cc_final: 0.8590 (p0) REVERT: B 359 GLU cc_start: 0.8788 (pt0) cc_final: 0.8402 (pp20) REVERT: B 438 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8380 (mm-40) REVERT: B 439 MET cc_start: 0.7948 (mmp) cc_final: 0.7684 (pp-130) REVERT: C 129 MET cc_start: 0.7403 (ptm) cc_final: 0.7021 (ttp) REVERT: C 185 LYS cc_start: 0.8806 (tptt) cc_final: 0.8458 (tmmt) REVERT: C 340 GLU cc_start: 0.8171 (pt0) cc_final: 0.7824 (pm20) outliers start: 23 outliers final: 13 residues processed: 116 average time/residue: 0.6110 time to fit residues: 76.2781 Evaluate side-chains 109 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 450 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 66 optimal weight: 0.0470 chunk 109 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074155 restraints weight = 16735.134| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.62 r_work: 0.2907 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10278 Z= 0.155 Angle : 0.649 11.164 13911 Z= 0.318 Chirality : 0.041 0.164 1490 Planarity : 0.003 0.041 1808 Dihedral : 4.770 27.778 1365 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.37 % Allowed : 15.74 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.86 (0.25), residues: 1245 helix: 1.70 (0.26), residues: 419 sheet: -0.79 (0.29), residues: 278 loop : 0.62 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 201 TYR 0.011 0.001 TYR B 417 PHE 0.017 0.001 PHE A 442 TRP 0.015 0.001 TRP A 46 HIS 0.002 0.000 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00357 (10257) covalent geometry : angle 0.63608 (13869) SS BOND : bond 0.00420 ( 21) SS BOND : angle 2.45253 ( 42) hydrogen bonds : bond 0.03765 ( 488) hydrogen bonds : angle 5.57290 ( 1446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9166 (tppt) cc_final: 0.8891 (tptp) REVERT: A 145 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8503 (mpp80) REVERT: A 340 GLU cc_start: 0.8539 (tp30) cc_final: 0.8191 (mp0) REVERT: A 380 LYS cc_start: 0.8323 (tttp) cc_final: 0.7751 (ttmm) REVERT: A 439 MET cc_start: 0.8783 (tpp) cc_final: 0.8389 (ttp) REVERT: B 72 HIS cc_start: 0.9099 (m90) cc_final: 0.8860 (m-70) REVERT: B 136 GLU cc_start: 0.9130 (tp30) cc_final: 0.8769 (tm-30) REVERT: B 201 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8174 (mmp-170) REVERT: B 295 MET cc_start: 0.6026 (ptt) cc_final: 0.5319 (ppp) REVERT: B 303 ASP cc_start: 0.8518 (p0) cc_final: 0.7926 (m-30) REVERT: B 321 GLU cc_start: 0.8934 (tt0) cc_final: 0.8691 (tt0) REVERT: B 333 ASP cc_start: 0.8794 (p0) cc_final: 0.8577 (p0) REVERT: B 359 GLU cc_start: 0.8709 (pt0) cc_final: 0.8317 (pp20) REVERT: B 438 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8437 (mm-40) REVERT: B 439 MET cc_start: 0.7959 (mmp) cc_final: 0.7700 (pp-130) REVERT: C 129 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6966 (ttp) REVERT: C 185 LYS cc_start: 0.8778 (tptt) cc_final: 0.8439 (tmmt) REVERT: C 340 GLU cc_start: 0.8157 (pt0) cc_final: 0.7601 (pm20) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.6661 time to fit residues: 77.0907 Evaluate side-chains 104 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 450 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.074332 restraints weight = 16580.487| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.62 r_work: 0.2898 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10278 Z= 0.160 Angle : 0.646 10.456 13911 Z= 0.317 Chirality : 0.041 0.155 1490 Planarity : 0.003 0.048 1808 Dihedral : 4.728 29.153 1365 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.28 % Allowed : 16.01 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.90 (0.25), residues: 1245 helix: 1.71 (0.26), residues: 420 sheet: -0.74 (0.29), residues: 278 loop : 0.64 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 201 TYR 0.011 0.001 TYR B 426 PHE 0.009 0.001 PHE B 263 TRP 0.013 0.001 TRP A 46 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00370 (10257) covalent geometry : angle 0.63512 (13869) SS BOND : bond 0.00391 ( 21) SS BOND : angle 2.28200 ( 42) hydrogen bonds : bond 0.03683 ( 488) hydrogen bonds : angle 5.54100 ( 1446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 133 LYS cc_start: 0.9236 (tppt) cc_final: 0.8834 (tptp) REVERT: A 145 ARG cc_start: 0.8809 (mmm160) cc_final: 0.8565 (mpp80) REVERT: A 380 LYS cc_start: 0.8368 (tttp) cc_final: 0.7801 (ttmm) REVERT: A 439 MET cc_start: 0.8741 (tpp) cc_final: 0.8387 (ttp) REVERT: B 72 HIS cc_start: 0.9101 (m90) cc_final: 0.8861 (m-70) REVERT: B 136 GLU cc_start: 0.9131 (tp30) cc_final: 0.8777 (tm-30) REVERT: B 201 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8169 (mmp-170) REVERT: B 295 MET cc_start: 0.6035 (ptt) cc_final: 0.5327 (ppp) REVERT: B 303 ASP cc_start: 0.8530 (p0) cc_final: 0.7935 (m-30) REVERT: B 321 GLU cc_start: 0.8939 (tt0) cc_final: 0.8705 (tt0) REVERT: B 333 ASP cc_start: 0.8804 (p0) cc_final: 0.8587 (p0) REVERT: B 359 GLU cc_start: 0.8685 (pt0) cc_final: 0.8297 (pp20) REVERT: B 438 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8459 (mm-40) REVERT: B 439 MET cc_start: 0.8039 (mmp) cc_final: 0.7807 (pp-130) REVERT: C 129 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6868 (ttp) REVERT: C 185 LYS cc_start: 0.8808 (tptt) cc_final: 0.8469 (tmmt) REVERT: C 340 GLU cc_start: 0.7980 (pt0) cc_final: 0.7659 (pm20) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.6365 time to fit residues: 71.0935 Evaluate side-chains 105 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 450 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 chunk 16 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN C 70 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075373 restraints weight = 16658.938| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.64 r_work: 0.2921 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10278 Z= 0.136 Angle : 0.632 9.811 13911 Z= 0.309 Chirality : 0.040 0.162 1490 Planarity : 0.003 0.041 1808 Dihedral : 4.652 28.273 1365 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.37 % Allowed : 16.10 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.90 (0.25), residues: 1245 helix: 1.71 (0.26), residues: 421 sheet: -0.71 (0.30), residues: 278 loop : 0.62 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 201 TYR 0.011 0.001 TYR B 417 PHE 0.016 0.001 PHE B 442 TRP 0.012 0.001 TRP A 46 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00311 (10257) covalent geometry : angle 0.62250 (13869) SS BOND : bond 0.00359 ( 21) SS BOND : angle 2.10263 ( 42) hydrogen bonds : bond 0.03605 ( 488) hydrogen bonds : angle 5.48340 ( 1446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3498.08 seconds wall clock time: 60 minutes 38.24 seconds (3638.24 seconds total)