Starting phenix.real_space_refine on Thu Jul 2 09:39:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8em2_28232/07_2026/8em2_28232.cif Found real_map, /net/cci-nas-00/data/ceres_data/8em2_28232/07_2026/8em2_28232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8em2_28232/07_2026/8em2_28232.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8em2_28232/07_2026/8em2_28232.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8em2_28232/07_2026/8em2_28232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8em2_28232/07_2026/8em2_28232.map" model { file = "/net/cci-nas-00/data/ceres_data/8em2_28232/07_2026/8em2_28232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8em2_28232/07_2026/8em2_28232.cif" } resolution = 3.02 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= 0.026 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 25 5.16 5 C 5120 2.51 5 N 1431 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8022 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4004 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3990 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 475} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.56, per 1000 atoms: 0.19 Number of scatterers: 8022 At special positions: 0 Unit cell: (81, 146.88, 81, 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 25 16.00 O 1446 8.00 N 1431 7.00 C 5120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 393 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 157 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 272.2 milliseconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 41.4% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.598A pdb=" N GLU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.993A pdb=" N GLN A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.559A pdb=" N ALA A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 removed outlier: 3.519A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 257 through 263 removed outlier: 4.104A pdb=" N ARG A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.785A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 324 removed outlier: 4.248A pdb=" N GLU A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.607A pdb=" N HIS A 385 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 456 through 468 removed outlier: 3.619A pdb=" N VAL A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 475 through 493 Proline residue: A 488 - end of helix Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.603A pdb=" N GLU A 506 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.404A pdb=" N LYS B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 53 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.511A pdb=" N GLU B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.952A pdb=" N SER B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.956A pdb=" N LEU B 206 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B 207 " --> pdb=" O HIS B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 207' Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.598A pdb=" N ASP B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 removed outlier: 4.465A pdb=" N GLU B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 removed outlier: 4.090A pdb=" N ARG B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.648A pdb=" N SER B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.691A pdb=" N PHE B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 315 through 324 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.797A pdb=" N TRP B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.537A pdb=" N LEU B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 110 removed outlier: 8.397A pdb=" N GLN A 107 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE A 62 " --> pdb=" O GLN A 107 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ARG A 109 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A 64 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 61 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N HIS A 25 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 137 " --> pdb=" O HIS A 25 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 171 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 140 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 170 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 202 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 172 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 201 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.065A pdb=" N GLN A 397 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY A 367 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE A 355 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 237 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N MET A 357 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE A 239 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY A 359 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N MET A 241 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ARG A 499 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 310 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR A 501 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 312 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.705A pdb=" N PHE B 513 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA5, first strand: chain 'A' and resid 519 through 522 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 110 removed outlier: 9.295A pdb=" N GLN B 107 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE B 62 " --> pdb=" O GLN B 107 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ARG B 109 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY B 64 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR B 200 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 411 through 414 removed outlier: 6.529A pdb=" N GLN B 397 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE B 373 " --> pdb=" O GLN B 397 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL B 399 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE B 371 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N HIS B 401 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 369 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 359 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AA9, first strand: chain 'B' and resid 437 through 438 323 hydrogen bonds defined for protein. 909 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: 0.94 Time building geometry restraints manager: 0.66 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: 2624 1.34 - 1.46: 1630 1.46 - 1.58: 3944 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 8236 Sorted by residual: bond pdb=" C LYS B 174 " pdb=" N PRO B 175 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.20e-02 6.94e+03 2.23e+01 bond pdb=" C1 NAG B 801 " pdb=" O5 NAG B 801 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.87e+00 bond pdb=" C LYS A 174 " pdb=" N PRO A 175 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.21e+00 bond pdb=" C SER A 441 " pdb=" N PRO A 442 " ideal model delta sigma weight residual 1.332 1.356 -0.024 1.34e-02 5.57e+03 3.25e+00 bond pdb=" CA LEU A 46 " pdb=" C LEU A 46 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.30e-02 5.92e+03 3.09e+00 ... (remaining 8231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 10867 2.15 - 4.29: 232 4.29 - 6.44: 36 6.44 - 8.58: 16 8.58 - 10.73: 3 Bond angle restraints: 11154 Sorted by residual: angle pdb=" N LEU B 206 " pdb=" CA LEU B 206 " pdb=" C LEU B 206 " ideal model delta sigma weight residual 113.72 104.30 9.42 1.30e+00 5.92e-01 5.25e+01 angle pdb=" C ASP A 219 " pdb=" N GLN A 220 " pdb=" CA GLN A 220 " ideal model delta sigma weight residual 122.56 115.27 7.29 1.72e+00 3.38e-01 1.80e+01 angle pdb=" CB GLU B 491 " pdb=" CG GLU B 491 " pdb=" CD GLU B 491 " ideal model delta sigma weight residual 112.60 118.88 -6.28 1.70e+00 3.46e-01 1.37e+01 angle pdb=" CA MET B 77 " pdb=" CB MET B 77 " pdb=" CG MET B 77 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB MET A 357 " pdb=" CG MET A 357 " pdb=" SD MET A 357 " ideal model delta sigma weight residual 112.70 123.43 -10.73 3.00e+00 1.11e-01 1.28e+01 ... (remaining 11149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4134 17.53 - 35.05: 538 35.05 - 52.58: 148 52.58 - 70.10: 22 70.10 - 87.63: 14 Dihedral angle restraints: 4856 sinusoidal: 1960 harmonic: 2896 Sorted by residual: dihedral pdb=" CA TYR A 446 " pdb=" C TYR A 446 " pdb=" N TYR A 447 " pdb=" CA TYR A 447 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLY B 403 " pdb=" C GLY B 403 " pdb=" N HIS B 404 " pdb=" CA HIS B 404 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA TYR A 41 " pdb=" C TYR A 41 " pdb=" N LEU A 42 " pdb=" CA LEU A 42 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 778 0.043 - 0.085: 291 0.085 - 0.128: 80 0.128 - 0.170: 25 0.170 - 0.213: 5 Chirality restraints: 1179 Sorted by residual: chirality pdb=" CB VAL A 237 " pdb=" CA VAL A 237 " pdb=" CG1 VAL A 237 " pdb=" CG2 VAL A 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL A 271 " pdb=" CA VAL A 271 " pdb=" CG1 VAL A 271 " pdb=" CG2 VAL A 271 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CB THR A 188 " pdb=" CA THR A 188 " pdb=" OG1 THR A 188 " pdb=" CG2 THR A 188 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 1176 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 144 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO A 145 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 130 " -0.015 2.00e-02 2.50e+03 2.16e-02 7.00e+00 pdb=" CG HIS A 130 " 0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS A 130 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS A 130 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS A 130 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 130 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 50 " 0.013 2.00e-02 2.50e+03 1.87e-02 7.00e+00 pdb=" CG TYR B 50 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 50 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 50 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 50 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 50 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 50 " -0.001 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1343 2.77 - 3.30: 7117 3.30 - 3.83: 13549 3.83 - 4.37: 15564 4.37 - 4.90: 27142 Nonbonded interactions: 64715 Sorted by model distance: nonbonded pdb=" O TRP A 483 " pdb=" OG1 THR A 487 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU A 514 " pdb=" OG SER A 523 " model vdw 2.270 3.040 nonbonded pdb=" OG SER B 252 " pdb=" OE1 GLU B 323 " model vdw 2.278 3.040 nonbonded pdb=" O LEU A 264 " pdb=" OG1 THR A 269 " model vdw 2.283 3.040 nonbonded pdb=" O TRP B 483 " pdb=" OG1 THR B 487 " model vdw 2.286 3.040 ... (remaining 64710 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 24 through 55 or resid 58 through 70 or (resid 71 and (nam \ e N or name CA or name C or name O or name CB )) or resid 72 through 81 or (resi \ d 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throug \ h 149 or (resid 150 and (name N or name CA or name C or name O or name CB )) or \ resid 151 through 525 or resid 801)) selection = (chain 'B' and (resid 24 through 67 or (resid 68 through 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 88 or resid 91 through \ 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 through 128 or (resid 129 and (name N or name CA or name C or name O or n \ ame CB )) or resid 130 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 299 or (resid 300 and (name N or \ name CA or name C or name O or name CB )) or resid 301 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.530 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8239 Z= 0.220 Angle : 0.820 10.728 11161 Z= 0.439 Chirality : 0.050 0.213 1179 Planarity : 0.006 0.067 1462 Dihedral : 17.394 87.629 2984 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.48 % Allowed : 22.16 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.24), residues: 994 helix: -1.69 (0.23), residues: 348 sheet: -0.18 (0.44), residues: 161 loop : -1.24 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.045 0.003 TYR B 50 PHE 0.041 0.003 PHE A 147 TRP 0.025 0.002 TRP B 229 HIS 0.028 0.002 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 ( 8236) covalent geometry : angle 0.81900 / 0.44 (11154) SS BOND : bond 0.00426 / 0.22 ( 2) SS BOND : angle 0.52513 / 0.30 ( 4) hydrogen bonds : bond 0.15850 / 10.49 ( 323) hydrogen bonds : angle 6.88036 / 5.02 ( 909) link_NAG-ASN : bond 0.00497 / 0.26 ( 1) link_NAG-ASN : angle 2.85994 / 1.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5879 (tmm) REVERT: A 115 GLU cc_start: 0.8228 (pm20) cc_final: 0.7954 (pm20) REVERT: A 120 LEU cc_start: 0.8191 (mp) cc_final: 0.7986 (mt) REVERT: A 223 LYS cc_start: 0.7336 (mppt) cc_final: 0.7092 (tptt) REVERT: A 277 MET cc_start: 0.7205 (ttt) cc_final: 0.6949 (ptm) REVERT: A 453 ARG cc_start: 0.7606 (ttp-110) cc_final: 0.7107 (tmm-80) REVERT: A 454 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6800 (tp30) REVERT: A 469 ARG cc_start: 0.7303 (mtt90) cc_final: 0.6939 (mtt90) REVERT: B 77 MET cc_start: 0.6930 (ppp) cc_final: 0.5900 (tmm) outliers start: 4 outliers final: 1 residues processed: 115 average time/residue: 0.0684 time to fit residues: 11.0394 Evaluate side-chains 97 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0060 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 110 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 314 GLN A 478 ASN A 524 GLN B 107 GLN B 110 GLN B 221 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.190474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.160215 restraints weight = 11641.339| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.42 r_work: 0.4096 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8239 Z= 0.139 Angle : 0.598 7.585 11161 Z= 0.307 Chirality : 0.042 0.151 1179 Planarity : 0.005 0.054 1462 Dihedral : 5.481 53.983 1098 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.04 % Allowed : 21.68 % Favored : 76.29 % 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: -0.88 (0.26), residues: 994 helix: -0.36 (0.27), residues: 354 sheet: -0.09 (0.44), residues: 158 loop : -0.83 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.016 0.002 TYR B 41 PHE 0.025 0.002 PHE A 253 TRP 0.008 0.001 TRP B 349 HIS 0.007 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8236) covalent geometry : angle 0.59697 / 0.31 (11154) SS BOND : bond 0.00151 / 0.08 ( 2) SS BOND : angle 0.38915 / 0.22 ( 4) hydrogen bonds : bond 0.04144 / 2.70 ( 323) hydrogen bonds : angle 5.17339 / 3.75 ( 909) link_NAG-ASN : bond 0.00093 / 0.05 ( 1) link_NAG-ASN : angle 2.53287 / 1.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6294 (tmm) REVERT: A 120 LEU cc_start: 0.8072 (mp) cc_final: 0.7721 (mp) REVERT: A 337 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6258 (t80) REVERT: A 454 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7002 (tp30) REVERT: A 469 ARG cc_start: 0.7550 (mtt90) cc_final: 0.7242 (mtt90) REVERT: B 77 MET cc_start: 0.6716 (ppp) cc_final: 0.5832 (tmm) REVERT: B 499 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.4890 (ttt180) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.0636 time to fit residues: 9.3881 Evaluate side-chains 98 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 499 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 38 optimal weight: 0.0040 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.188839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.158355 restraints weight = 11705.389| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.56 r_work: 0.4041 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8239 Z= 0.135 Angle : 0.575 7.166 11161 Z= 0.292 Chirality : 0.042 0.153 1179 Planarity : 0.005 0.086 1462 Dihedral : 5.385 59.645 1098 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.47 % Allowed : 21.68 % Favored : 74.85 % 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: -0.44 (0.27), residues: 994 helix: 0.17 (0.28), residues: 356 sheet: 0.09 (0.45), residues: 152 loop : -0.68 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 109 TYR 0.014 0.001 TYR A 446 PHE 0.019 0.002 PHE A 147 TRP 0.008 0.002 TRP A 43 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 8236) covalent geometry : angle 0.57397 / 0.29 (11154) SS BOND : bond 0.00142 / 0.07 ( 2) SS BOND : angle 0.34885 / 0.20 ( 4) hydrogen bonds : bond 0.03626 / 2.33 ( 323) hydrogen bonds : angle 4.83912 / 3.49 ( 909) link_NAG-ASN : bond 0.00117 / 0.06 ( 1) link_NAG-ASN : angle 2.41448 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6419 (tmm) REVERT: A 120 LEU cc_start: 0.8347 (mp) cc_final: 0.7891 (mt) REVERT: A 220 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.5344 (mm-40) REVERT: A 255 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5408 (tm-30) REVERT: A 337 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.6205 (t80) REVERT: A 453 ARG cc_start: 0.8059 (tmm-80) cc_final: 0.7803 (mtm-85) REVERT: A 454 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6992 (tp30) REVERT: A 469 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7247 (mtt90) REVERT: B 77 MET cc_start: 0.6557 (ppp) cc_final: 0.5945 (tmm) REVERT: B 95 CYS cc_start: 0.3396 (OUTLIER) cc_final: 0.2187 (m) REVERT: B 314 GLN cc_start: 0.7436 (tm-30) cc_final: 0.6464 (tm-30) REVERT: B 392 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.6304 (mm-40) outliers start: 29 outliers final: 14 residues processed: 114 average time/residue: 0.0650 time to fit residues: 10.5982 Evaluate side-chains 101 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 24 optimal weight: 0.7980 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.184742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.154138 restraints weight = 12064.049| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.57 r_work: 0.3989 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8239 Z= 0.217 Angle : 0.668 7.791 11161 Z= 0.340 Chirality : 0.045 0.165 1179 Planarity : 0.005 0.047 1462 Dihedral : 5.642 56.973 1098 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.47 % Allowed : 21.92 % Favored : 74.61 % 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: -0.58 (0.27), residues: 994 helix: 0.22 (0.29), residues: 344 sheet: 0.07 (0.45), residues: 146 loop : -0.91 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 455 TYR 0.020 0.002 TYR A 446 PHE 0.018 0.002 PHE B 354 TRP 0.011 0.002 TRP A 167 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 ( 8236) covalent geometry : angle 0.66583 / 0.34 (11154) SS BOND : bond 0.00284 / 0.15 ( 2) SS BOND : angle 0.41203 / 0.24 ( 4) hydrogen bonds : bond 0.04191 / 2.69 ( 323) hydrogen bonds : angle 4.93634 / 3.54 ( 909) link_NAG-ASN : bond 0.00051 / 0.03 ( 1) link_NAG-ASN : angle 3.10290 / 1.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6471 (tmm) REVERT: A 255 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.5441 (tm-30) REVERT: A 272 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7191 (tp) REVERT: A 293 LYS cc_start: 0.6932 (tttm) cc_final: 0.6184 (tttt) REVERT: A 337 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.6215 (t80) REVERT: A 453 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7677 (tmm-80) REVERT: A 454 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7123 (tp30) REVERT: B 95 CYS cc_start: 0.3508 (OUTLIER) cc_final: 0.2200 (m) REVERT: B 265 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7113 (tp40) REVERT: B 314 GLN cc_start: 0.7563 (tm-30) cc_final: 0.6625 (tm-30) REVERT: B 392 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.6337 (mm-40) outliers start: 29 outliers final: 17 residues processed: 115 average time/residue: 0.0594 time to fit residues: 9.8567 Evaluate side-chains 110 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.189849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.159686 restraints weight = 11737.797| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.43 r_work: 0.4074 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8239 Z= 0.111 Angle : 0.567 12.358 11161 Z= 0.283 Chirality : 0.042 0.158 1179 Planarity : 0.004 0.051 1462 Dihedral : 5.239 54.615 1098 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.23 % Allowed : 21.92 % Favored : 74.85 % 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: -0.26 (0.28), residues: 994 helix: 0.51 (0.29), residues: 344 sheet: 0.23 (0.46), residues: 145 loop : -0.73 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.012 0.001 TYR A 313 PHE 0.024 0.001 PHE A 253 TRP 0.010 0.001 TRP B 229 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 8236) covalent geometry : angle 0.56647 / 0.28 (11154) SS BOND : bond 0.00127 / 0.07 ( 2) SS BOND : angle 0.30725 / 0.18 ( 4) hydrogen bonds : bond 0.03389 / 2.21 ( 323) hydrogen bonds : angle 4.71178 / 3.39 ( 909) link_NAG-ASN : bond 0.00189 / 0.10 ( 1) link_NAG-ASN : angle 1.98530 / 1.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.6694 (tp40) cc_final: 0.6464 (mm-40) REVERT: A 120 LEU cc_start: 0.8404 (mp) cc_final: 0.8141 (mt) REVERT: A 220 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.5638 (tp-100) REVERT: A 255 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5307 (tm-30) REVERT: A 454 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7131 (tp30) REVERT: B 95 CYS cc_start: 0.3447 (OUTLIER) cc_final: 0.2191 (m) REVERT: B 265 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6758 (tp40) REVERT: B 314 GLN cc_start: 0.7529 (tm-30) cc_final: 0.6539 (tm-30) REVERT: B 392 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6117 (mm-40) outliers start: 27 outliers final: 12 residues processed: 112 average time/residue: 0.0853 time to fit residues: 13.3754 Evaluate side-chains 107 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.187898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.157646 restraints weight = 11595.663| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.42 r_work: 0.4074 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8239 Z= 0.117 Angle : 0.576 15.260 11161 Z= 0.285 Chirality : 0.042 0.171 1179 Planarity : 0.004 0.049 1462 Dihedral : 4.927 48.435 1095 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.83 % Allowed : 21.92 % Favored : 74.25 % 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: -0.22 (0.28), residues: 994 helix: 0.59 (0.29), residues: 347 sheet: 0.28 (0.46), residues: 146 loop : -0.75 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 455 TYR 0.015 0.001 TYR B 41 PHE 0.017 0.001 PHE A 253 TRP 0.009 0.001 TRP A 43 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8236) covalent geometry : angle 0.57568 / 0.29 (11154) SS BOND : bond 0.00178 / 0.09 ( 2) SS BOND : angle 0.27849 / 0.16 ( 4) hydrogen bonds : bond 0.03362 / 2.19 ( 323) hydrogen bonds : angle 4.68584 / 3.37 ( 909) link_NAG-ASN : bond 0.00161 / 0.08 ( 1) link_NAG-ASN : angle 1.84980 / 0.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8407 (mp) cc_final: 0.8126 (mt) REVERT: A 220 GLN cc_start: 0.6660 (mp10) cc_final: 0.5620 (tp-100) REVERT: A 255 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5278 (tm-30) REVERT: A 270 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: A 454 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7132 (tp30) REVERT: A 514 GLU cc_start: 0.5149 (OUTLIER) cc_final: 0.4231 (mp0) REVERT: B 28 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7590 (mp) REVERT: B 215 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7602 (mp) REVERT: B 265 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6753 (tp40) REVERT: B 314 GLN cc_start: 0.7505 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 392 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.6103 (mm-40) REVERT: B 499 ARG cc_start: 0.5184 (OUTLIER) cc_final: 0.4759 (ttm-80) outliers start: 32 outliers final: 18 residues processed: 120 average time/residue: 0.0662 time to fit residues: 11.0001 Evaluate side-chains 114 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 23 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.189394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.159301 restraints weight = 11761.871| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.43 r_work: 0.4093 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8239 Z= 0.102 Angle : 0.560 14.983 11161 Z= 0.277 Chirality : 0.041 0.168 1179 Planarity : 0.004 0.049 1462 Dihedral : 4.740 49.656 1095 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.95 % Allowed : 21.56 % Favored : 74.49 % 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: -0.09 (0.28), residues: 994 helix: 0.72 (0.29), residues: 348 sheet: 0.31 (0.46), residues: 146 loop : -0.69 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.012 0.001 TYR A 313 PHE 0.013 0.001 PHE A 253 TRP 0.010 0.001 TRP B 229 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 8236) covalent geometry : angle 0.55965 / 0.28 (11154) SS BOND : bond 0.00090 / 0.05 ( 2) SS BOND : angle 0.23669 / 0.14 ( 4) hydrogen bonds : bond 0.03149 / 2.08 ( 323) hydrogen bonds : angle 4.57274 / 3.30 ( 909) link_NAG-ASN : bond 0.00225 / 0.12 ( 1) link_NAG-ASN : angle 1.47882 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.6668 (tp40) cc_final: 0.6401 (mm-40) REVERT: A 77 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6211 (tmm) REVERT: A 120 LEU cc_start: 0.8435 (mp) cc_final: 0.8203 (mt) REVERT: A 220 GLN cc_start: 0.6552 (mt0) cc_final: 0.5524 (tp-100) REVERT: A 255 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5274 (tm-30) REVERT: A 454 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7100 (tp30) REVERT: A 514 GLU cc_start: 0.5032 (OUTLIER) cc_final: 0.4149 (mp0) REVERT: B 265 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6591 (tp40) REVERT: B 499 ARG cc_start: 0.5144 (OUTLIER) cc_final: 0.4722 (ttm-80) outliers start: 33 outliers final: 21 residues processed: 117 average time/residue: 0.0659 time to fit residues: 10.6817 Evaluate side-chains 113 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 233 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.186403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.155892 restraints weight = 11782.742| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.43 r_work: 0.4049 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8239 Z= 0.154 Angle : 0.615 14.993 11161 Z= 0.305 Chirality : 0.043 0.173 1179 Planarity : 0.004 0.046 1462 Dihedral : 4.997 49.764 1095 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.19 % Allowed : 20.96 % Favored : 74.85 % 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: -0.24 (0.28), residues: 994 helix: 0.62 (0.29), residues: 348 sheet: 0.16 (0.45), residues: 146 loop : -0.78 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.017 0.002 TYR A 446 PHE 0.033 0.002 PHE A 253 TRP 0.010 0.002 TRP B 486 HIS 0.004 0.001 HIS B 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 8236) covalent geometry : angle 0.61405 / 0.31 (11154) SS BOND : bond 0.00213 / 0.11 ( 2) SS BOND : angle 0.21512 / 0.13 ( 4) hydrogen bonds : bond 0.03538 / 2.29 ( 323) hydrogen bonds : angle 4.67735 / 3.37 ( 909) link_NAG-ASN : bond 0.00086 / 0.05 ( 1) link_NAG-ASN : angle 2.03787 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 23 GLN cc_start: 0.6647 (tp40) cc_final: 0.6396 (mm-40) REVERT: A 77 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6095 (tmm) REVERT: A 120 LEU cc_start: 0.8482 (mp) cc_final: 0.8211 (mt) REVERT: A 220 GLN cc_start: 0.6590 (mt0) cc_final: 0.5645 (tp-100) REVERT: A 255 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.5373 (tm-30) REVERT: A 257 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.5967 (t80) REVERT: A 270 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: A 454 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7129 (tp30) REVERT: A 514 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4187 (mp0) REVERT: B 28 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 265 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7039 (tp40) REVERT: B 314 GLN cc_start: 0.7561 (tm-30) cc_final: 0.6657 (tm-30) REVERT: B 392 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.6247 (mm-40) REVERT: B 499 ARG cc_start: 0.5205 (OUTLIER) cc_final: 0.4722 (ttm-80) outliers start: 35 outliers final: 23 residues processed: 120 average time/residue: 0.0638 time to fit residues: 10.7752 Evaluate side-chains 122 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 229 TRP Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 0.0040 chunk 97 optimal weight: 0.0000 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.191750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.161936 restraints weight = 11526.176| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.41 r_work: 0.4096 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8239 Z= 0.100 Angle : 0.563 13.526 11161 Z= 0.277 Chirality : 0.041 0.155 1179 Planarity : 0.004 0.051 1462 Dihedral : 4.744 50.801 1095 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.99 % Allowed : 22.51 % Favored : 74.49 % 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: -0.05 (0.28), residues: 994 helix: 0.74 (0.29), residues: 354 sheet: 0.27 (0.46), residues: 146 loop : -0.65 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 455 TYR 0.015 0.001 TYR B 41 PHE 0.028 0.001 PHE A 253 TRP 0.012 0.001 TRP B 229 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 8236) covalent geometry : angle 0.56247 / 0.28 (11154) SS BOND : bond 0.00131 / 0.07 ( 2) SS BOND : angle 0.23915 / 0.14 ( 4) hydrogen bonds : bond 0.03036 / 1.99 ( 323) hydrogen bonds : angle 4.52047 / 3.27 ( 909) link_NAG-ASN : bond 0.00216 / 0.11 ( 1) link_NAG-ASN : angle 1.55752 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.193 Fit side-chains REVERT: A 23 GLN cc_start: 0.6711 (tp40) cc_final: 0.6499 (mm-40) REVERT: A 77 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6020 (tmm) REVERT: A 120 LEU cc_start: 0.8452 (mp) cc_final: 0.8160 (mt) REVERT: A 220 GLN cc_start: 0.6523 (mt0) cc_final: 0.5636 (tp-100) REVERT: A 255 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5339 (tm-30) REVERT: A 257 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.5822 (t80) REVERT: A 454 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7066 (tp30) REVERT: A 514 GLU cc_start: 0.5034 (OUTLIER) cc_final: 0.4138 (mp0) REVERT: B 265 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6627 (tp40) REVERT: B 314 GLN cc_start: 0.7487 (tm-30) cc_final: 0.6619 (tm-30) REVERT: B 499 ARG cc_start: 0.5154 (OUTLIER) cc_final: 0.4651 (ttm-80) outliers start: 25 outliers final: 17 residues processed: 111 average time/residue: 0.0670 time to fit residues: 10.2982 Evaluate side-chains 111 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 499 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.190091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.160085 restraints weight = 11707.826| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.42 r_work: 0.4071 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8239 Z= 0.124 Angle : 0.592 14.218 11161 Z= 0.295 Chirality : 0.042 0.169 1179 Planarity : 0.004 0.050 1462 Dihedral : 4.821 50.891 1095 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.99 % Allowed : 22.40 % Favored : 74.61 % 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: -0.10 (0.28), residues: 994 helix: 0.74 (0.29), residues: 347 sheet: 0.12 (0.45), residues: 153 loop : -0.66 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 455 TYR 0.013 0.001 TYR A 446 PHE 0.028 0.001 PHE A 253 TRP 0.008 0.001 TRP B 486 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8236) covalent geometry : angle 0.59138 / 0.29 (11154) SS BOND : bond 0.00155 / 0.08 ( 2) SS BOND : angle 0.29878 / 0.18 ( 4) hydrogen bonds : bond 0.03260 / 2.11 ( 323) hydrogen bonds : angle 4.58745 / 3.30 ( 909) link_NAG-ASN : bond 0.00150 / 0.08 ( 1) link_NAG-ASN : angle 1.77088 / 0.91 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.290 Fit side-chains REVERT: A 23 GLN cc_start: 0.6747 (tp40) cc_final: 0.6544 (mm-40) REVERT: A 77 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6210 (tmm) REVERT: A 120 LEU cc_start: 0.8438 (mp) cc_final: 0.8165 (mt) REVERT: A 220 GLN cc_start: 0.6614 (mt0) cc_final: 0.5701 (tp-100) REVERT: A 255 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5341 (tm-30) REVERT: A 257 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5927 (t80) REVERT: A 270 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: A 454 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7090 (tp30) REVERT: A 514 GLU cc_start: 0.5086 (OUTLIER) cc_final: 0.4189 (mp0) REVERT: B 265 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6766 (tp40) REVERT: B 314 GLN cc_start: 0.7493 (tm-30) cc_final: 0.6609 (tm-30) REVERT: B 499 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.4771 (ttm-80) outliers start: 25 outliers final: 16 residues processed: 106 average time/residue: 0.0722 time to fit residues: 10.6833 Evaluate side-chains 110 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 205 TYR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 499 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.190129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.159845 restraints weight = 11752.670| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.48 r_work: 0.4066 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8239 Z= 0.124 Angle : 0.593 13.449 11161 Z= 0.298 Chirality : 0.043 0.212 1179 Planarity : 0.004 0.049 1462 Dihedral : 4.864 51.082 1095 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.59 % Allowed : 22.04 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.28), residues: 994 helix: 0.67 (0.29), residues: 353 sheet: 0.15 (0.45), residues: 153 loop : -0.65 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 305 TYR 0.015 0.002 TYR B 41 PHE 0.015 0.001 PHE B 515 TRP 0.008 0.001 TRP B 486 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 8236) covalent geometry : angle 0.59262 / 0.30 (11154) SS BOND : bond 0.00157 / 0.08 ( 2) SS BOND : angle 0.29048 / 0.17 ( 4) hydrogen bonds : bond 0.03343 / 2.15 ( 323) hydrogen bonds : angle 4.65749 / 3.33 ( 909) link_NAG-ASN : bond 0.00167 / 0.09 ( 1) link_NAG-ASN : angle 1.79277 / 0.92 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.17 seconds wall clock time: 26 minutes 16.36 seconds (1576.36 seconds total)