Starting phenix.real_space_refine on Wed Mar 4 04:51:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ou9_20198/03_2026/6ou9_20198.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ou9_20198/03_2026/6ou9_20198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ou9_20198/03_2026/6ou9_20198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ou9_20198/03_2026/6ou9_20198.map" model { file = "/net/cci-nas-00/data/ceres_data/6ou9_20198/03_2026/6ou9_20198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ou9_20198/03_2026/6ou9_20198.cif" } resolution = 3.2 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= 0.005 sd= 0.086 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 57 5.16 5 C 7211 2.51 5 N 1916 2.21 5 O 2085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11269 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3865 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 51, 'TRANS': 455} Chain breaks: 1 Chain: "A" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3703 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 49, 'TRANS': 433} Chain breaks: 2 Chain: "C" Number of atoms: 3701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3701 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 49, 'TRANS': 433} Chain breaks: 2 Time building chain proxies: 2.58, per 1000 atoms: 0.23 Number of scatterers: 11269 At special positions: 0 Unit cell: (102.72, 109.14, 111.28, 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 57 16.00 O 2085 8.00 N 1916 7.00 C 7211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.85 Conformation dependent library (CDL) restraints added in 582.7 milliseconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 19 sheets defined 8.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.957A pdb=" N ALA B 45 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 46 " --> pdb=" O THR B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.961A pdb=" N LEU B 91 " --> pdb=" O GLY B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.682A pdb=" N GLN B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.555A pdb=" N THR B 145 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.581A pdb=" N HIS B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 459 " --> pdb=" O PHE B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.822A pdb=" N ASN B 503 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.955A pdb=" N LEU A 91 " --> pdb=" O GLY A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 92 through 99 removed outlier: 3.586A pdb=" N HIS A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.778A pdb=" N PHE A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.577A pdb=" N GLU A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.692A pdb=" N ASN A 503 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 504 " --> pdb=" O PRO A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 504' Processing helix chain 'C' and resid 88 through 92 removed outlier: 4.018A pdb=" N LEU C 91 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 92' Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.715A pdb=" N THR C 229 " --> pdb=" O GLU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.529A pdb=" N VAL C 452 " --> pdb=" O PRO C 448 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 removed outlier: 3.513A pdb=" N ASN C 503 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 71 removed outlier: 12.384A pdb=" N GLN B 64 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 10.354A pdb=" N THR B 209 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY B 68 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 206 " --> pdb=" O MET B 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 164 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 81 through 86 removed outlier: 7.191A pdb=" N CYS B 185 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP B 84 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 183 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS B 124 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA B 122 " --> pdb=" O PRO B 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 106 removed outlier: 3.656A pdb=" N ASN B 216 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 251 through 255 removed outlier: 7.920A pdb=" N ILE B 251 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP B 432 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS B 253 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 290 through 296 removed outlier: 4.238A pdb=" N LYS B 302 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B 368 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS B 355 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 332 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 386 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS B 334 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.960A pdb=" N PHE B 490 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 466 " --> pdb=" O TRP B 515 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP B 515 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 468 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA8, first strand: chain 'A' and resid 63 through 64 removed outlier: 4.196A pdb=" N ALA A 204 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 86 removed outlier: 4.064A pdb=" N PHE A 83 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'A' and resid 251 through 255 removed outlier: 6.703A pdb=" N MET A 430 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET A 254 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR A 428 " --> pdb=" O MET A 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 349 through 354 removed outlier: 3.700A pdb=" N TRP A 385 " --> pdb=" O HIS A 334 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER A 336 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU A 383 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE A 338 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY A 381 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 302 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 369 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 425 through 426 removed outlier: 4.083A pdb=" N PHE A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 481 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 466 " --> pdb=" O TRP A 515 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TRP A 515 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 468 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 63 through 72 removed outlier: 12.388A pdb=" N GLN C 64 " --> pdb=" O PRO C 211 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N THR C 209 " --> pdb=" O PRO C 66 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLY C 68 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 81 through 86 removed outlier: 6.983A pdb=" N CYS C 185 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP C 84 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 183 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 188 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS C 124 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 122 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB8, first strand: chain 'C' and resid 253 through 255 removed outlier: 4.204A pdb=" N LYS C 253 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 290 through 297 removed outlier: 4.453A pdb=" N LYS C 302 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU C 368 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS C 355 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP C 385 " --> pdb=" O HIS C 334 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER C 336 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU C 383 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N PHE C 338 " --> pdb=" O GLY C 381 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY C 381 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 425 through 426 removed outlier: 6.484A pdb=" N TYR C 471 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU C 482 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 469 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS C 484 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 467 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA C 466 " --> pdb=" O TRP C 515 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP C 515 " --> pdb=" O ALA C 466 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU C 468 " --> pdb=" O SER C 513 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 624 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: 1.71 Time building geometry restraints manager: 1.20 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: 3676 1.34 - 1.45: 1753 1.45 - 1.57: 6077 1.57 - 1.69: 0 1.69 - 1.80: 90 Bond restraints: 11596 Sorted by residual: bond pdb=" N ARG C 178 " pdb=" CA ARG C 178 " ideal model delta sigma weight residual 1.456 1.427 0.029 1.48e-02 4.57e+03 3.75e+00 bond pdb=" CB VAL C 106 " pdb=" CG1 VAL C 106 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.21e+00 bond pdb=" C ILE C 400 " pdb=" N PRO C 401 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.25e-02 6.40e+03 1.36e+00 bond pdb=" C ALA C 65 " pdb=" N PRO C 66 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" C SER B 73 " pdb=" N PRO B 74 " ideal model delta sigma weight residual 1.334 1.343 -0.010 8.40e-03 1.42e+04 1.33e+00 ... (remaining 11591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 15280 1.76 - 3.53: 525 3.53 - 5.29: 62 5.29 - 7.06: 11 7.06 - 8.82: 3 Bond angle restraints: 15881 Sorted by residual: angle pdb=" C VAL B 221 " pdb=" CA VAL B 221 " pdb=" CB VAL B 221 " ideal model delta sigma weight residual 109.33 115.00 -5.67 9.80e-01 1.04e+00 3.34e+01 angle pdb=" N VAL B 340 " pdb=" CA VAL B 340 " pdb=" C VAL B 340 " ideal model delta sigma weight residual 113.07 106.72 6.35 1.37e+00 5.33e-01 2.15e+01 angle pdb=" N VAL B 221 " pdb=" CA VAL B 221 " pdb=" C VAL B 221 " ideal model delta sigma weight residual 109.19 105.90 3.29 8.20e-01 1.49e+00 1.61e+01 angle pdb=" CA VAL B 221 " pdb=" C VAL B 221 " pdb=" N PRO B 222 " ideal model delta sigma weight residual 116.57 119.95 -3.38 9.80e-01 1.04e+00 1.19e+01 angle pdb=" N ARG C 178 " pdb=" CA ARG C 178 " pdb=" C ARG C 178 " ideal model delta sigma weight residual 107.95 100.88 7.07 2.14e+00 2.18e-01 1.09e+01 ... (remaining 15876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6324 17.44 - 34.89: 463 34.89 - 52.33: 89 52.33 - 69.77: 12 69.77 - 87.22: 7 Dihedral angle restraints: 6895 sinusoidal: 2693 harmonic: 4202 Sorted by residual: dihedral pdb=" CA PHE C 217 " pdb=" C PHE C 217 " pdb=" N LEU C 218 " pdb=" CA LEU C 218 " ideal model delta harmonic sigma weight residual 180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL C 340 " pdb=" C VAL C 340 " pdb=" N ASP C 341 " pdb=" CA ASP C 341 " ideal model delta harmonic sigma weight residual 180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ARG A 182 " pdb=" C ARG A 182 " pdb=" N LEU A 183 " pdb=" CA LEU A 183 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 954 0.035 - 0.070: 504 0.070 - 0.104: 180 0.104 - 0.139: 122 0.139 - 0.174: 23 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CB THR A 497 " pdb=" CA THR A 497 " pdb=" OG1 THR A 497 " pdb=" CG2 THR A 497 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA VAL C 256 " pdb=" N VAL C 256 " pdb=" C VAL C 256 " pdb=" CB VAL C 256 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CB ILE B 126 " pdb=" CA ILE B 126 " pdb=" CG1 ILE B 126 " pdb=" CG2 ILE B 126 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1780 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 212 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO A 213 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 212 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 213 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 212 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO C 213 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 213 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 213 " 0.041 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 106 2.63 - 3.20: 8951 3.20 - 3.77: 15624 3.77 - 4.33: 22055 4.33 - 4.90: 37821 Nonbonded interactions: 84557 Sorted by model distance: nonbonded pdb=" NH2 ARG C 394 " pdb=" OD1 ASN C 439 " model vdw 2.067 3.120 nonbonded pdb=" NZ LYS A 294 " pdb=" OD2 ASP A 378 " model vdw 2.265 3.120 nonbonded pdb=" CE LYS A 294 " pdb=" OD2 ASP A 378 " model vdw 2.300 3.440 nonbonded pdb=" O ASN C 108 " pdb=" OG SER C 212 " model vdw 2.310 3.040 nonbonded pdb=" OG SER C 319 " pdb=" O ALA C 321 " model vdw 2.330 3.040 ... (remaining 84552 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 33 through 404 or resid 412 through 526)) selection = (chain 'B' and (resid 33 through 404 or resid 412 through 526)) selection = (chain 'C' and (resid 33 through 193 or resid 200 through 404 or resid 412 throu \ gh 526)) } 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: 0.050 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: 0.040 Set scattering table: 0.030 Process input model: 11.140 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.006 0.055 11596 Z= 0.248 Angle : 0.753 8.822 15881 Z= 0.430 Chirality : 0.054 0.174 1783 Planarity : 0.009 0.084 2112 Dihedral : 12.958 87.217 4185 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -3.26 (0.18), residues: 1457 helix: -4.17 (0.26), residues: 71 sheet: -1.49 (0.24), residues: 387 loop : -2.44 (0.16), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 518 TYR 0.009 0.002 TYR A 102 PHE 0.027 0.002 PHE C 83 TRP 0.011 0.001 TRP C 385 HIS 0.003 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00582 (11596) covalent geometry : angle 0.75276 (15881) hydrogen bonds : bond 0.25834 ( 246) hydrogen bonds : angle 9.72152 ( 624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.398 Fit side-chains REVERT: B 57 TRP cc_start: 0.8875 (m100) cc_final: 0.8604 (m100) REVERT: B 192 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7414 (mtt180) REVERT: B 308 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8405 (mm-30) REVERT: B 430 MET cc_start: 0.8966 (mmm) cc_final: 0.8563 (mmm) REVERT: A 252 ASN cc_start: 0.8622 (t0) cc_final: 0.8374 (t0) REVERT: A 396 ASP cc_start: 0.8761 (t0) cc_final: 0.8511 (t0) REVERT: A 458 GLN cc_start: 0.8465 (tt0) cc_final: 0.8224 (tt0) REVERT: A 478 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7860 (mmm160) REVERT: C 290 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8330 (mmm-85) REVERT: C 338 PHE cc_start: 0.8077 (p90) cc_final: 0.7767 (p90) REVERT: C 349 MET cc_start: 0.8446 (mmm) cc_final: 0.8209 (mmm) REVERT: C 457 GLU cc_start: 0.7006 (tp30) cc_final: 0.6790 (tp30) REVERT: C 465 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7651 (mt-10) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1071 time to fit residues: 46.9052 Evaluate side-chains 262 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN B 315 HIS B 343 ASN A 60 ASN A 108 ASN A 357 ASN A 458 GLN C 75 ASN C 76 ASN C 86 HIS C 173 HIS C 479 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.083495 restraints weight = 16495.072| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.63 r_work: 0.2569 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11596 Z= 0.249 Angle : 0.615 9.526 15881 Z= 0.311 Chirality : 0.048 0.158 1783 Planarity : 0.007 0.060 2112 Dihedral : 5.035 22.919 1546 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.20 % Allowed : 9.02 % Favored : 89.78 % 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: -2.64 (0.19), residues: 1457 helix: -3.30 (0.38), residues: 79 sheet: -1.25 (0.24), residues: 395 loop : -1.93 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 206 TYR 0.009 0.001 TYR C 520 PHE 0.020 0.002 PHE C 83 TRP 0.009 0.001 TRP C 105 HIS 0.007 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00604 (11596) covalent geometry : angle 0.61519 (15881) hydrogen bonds : bond 0.04616 ( 246) hydrogen bonds : angle 6.48997 ( 624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 280 time to evaluate : 0.447 Fit side-chains REVERT: B 57 TRP cc_start: 0.9100 (m100) cc_final: 0.8821 (m100) REVERT: B 192 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.7480 (mtt180) REVERT: B 237 ILE cc_start: 0.9442 (mt) cc_final: 0.9078 (mm) REVERT: B 294 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7864 (mttp) REVERT: A 396 ASP cc_start: 0.8970 (t0) cc_final: 0.8637 (t0) REVERT: A 458 GLN cc_start: 0.8780 (tt0) cc_final: 0.8552 (tt0) REVERT: C 236 ASN cc_start: 0.8868 (t0) cc_final: 0.8590 (t0) REVERT: C 349 MET cc_start: 0.8651 (mmm) cc_final: 0.8373 (mmm) REVERT: C 465 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8391 (mt-10) REVERT: C 479 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7825 (t0) outliers start: 15 outliers final: 10 residues processed: 287 average time/residue: 0.0968 time to fit residues: 40.3798 Evaluate side-chains 270 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 259 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 479 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 76 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 130 optimal weight: 0.0570 chunk 86 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN C 90 HIS C 479 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.084648 restraints weight = 16603.208| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.66 r_work: 0.2729 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11596 Z= 0.116 Angle : 0.525 8.114 15881 Z= 0.261 Chirality : 0.046 0.157 1783 Planarity : 0.006 0.056 2112 Dihedral : 4.582 21.154 1546 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.96 % Allowed : 12.21 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.20), residues: 1457 helix: -2.82 (0.43), residues: 79 sheet: -0.83 (0.25), residues: 389 loop : -1.58 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 518 TYR 0.009 0.001 TYR C 520 PHE 0.016 0.001 PHE C 83 TRP 0.009 0.001 TRP A 385 HIS 0.014 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00282 (11596) covalent geometry : angle 0.52522 (15881) hydrogen bonds : bond 0.03373 ( 246) hydrogen bonds : angle 5.87231 ( 624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 275 time to evaluate : 0.405 Fit side-chains REVERT: B 28 ASN cc_start: 0.8892 (t0) cc_final: 0.8569 (t0) REVERT: B 57 TRP cc_start: 0.9102 (m100) cc_final: 0.8829 (m100) REVERT: B 192 ARG cc_start: 0.8353 (mmt-90) cc_final: 0.7483 (mtt180) REVERT: B 231 GLN cc_start: 0.8310 (tt0) cc_final: 0.7989 (tp40) REVERT: B 237 ILE cc_start: 0.9461 (mt) cc_final: 0.9109 (mm) REVERT: A 396 ASP cc_start: 0.8927 (t0) cc_final: 0.8620 (t0) REVERT: C 236 ASN cc_start: 0.8843 (t0) cc_final: 0.8615 (t0) REVERT: C 287 GLN cc_start: 0.9089 (mt0) cc_final: 0.8790 (mt0) REVERT: C 302 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7770 (tppt) REVERT: C 349 MET cc_start: 0.8690 (mmm) cc_final: 0.8440 (mmm) outliers start: 12 outliers final: 8 residues processed: 279 average time/residue: 0.0979 time to fit residues: 39.6485 Evaluate side-chains 269 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 261 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 114 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN A 236 ASN C 503 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.080783 restraints weight = 16791.905| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.72 r_work: 0.2684 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11596 Z= 0.192 Angle : 0.554 8.342 15881 Z= 0.275 Chirality : 0.047 0.156 1783 Planarity : 0.005 0.052 2112 Dihedral : 4.572 20.752 1546 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.15 % Allowed : 12.37 % Favored : 85.47 % 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: -1.83 (0.20), residues: 1457 helix: -2.57 (0.45), residues: 79 sheet: -0.68 (0.25), residues: 393 loop : -1.38 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 206 TYR 0.010 0.001 TYR C 520 PHE 0.016 0.001 PHE C 83 TRP 0.007 0.001 TRP C 385 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00472 (11596) covalent geometry : angle 0.55444 (15881) hydrogen bonds : bond 0.03478 ( 246) hydrogen bonds : angle 5.67189 ( 624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.467 Fit side-chains REVERT: B 57 TRP cc_start: 0.9091 (m100) cc_final: 0.8830 (m100) REVERT: B 192 ARG cc_start: 0.8377 (mmt-90) cc_final: 0.7531 (mtt180) REVERT: B 231 GLN cc_start: 0.8372 (tt0) cc_final: 0.8079 (tt0) REVERT: B 344 LEU cc_start: 0.8771 (mt) cc_final: 0.8501 (mt) REVERT: A 236 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8889 (t0) REVERT: A 396 ASP cc_start: 0.8948 (t0) cc_final: 0.8743 (t0) REVERT: C 80 ASP cc_start: 0.8867 (m-30) cc_final: 0.8654 (m-30) REVERT: C 236 ASN cc_start: 0.8929 (t0) cc_final: 0.8710 (t0) REVERT: C 302 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7670 (tppt) REVERT: C 349 MET cc_start: 0.8671 (mmm) cc_final: 0.8395 (mmm) outliers start: 27 outliers final: 18 residues processed: 275 average time/residue: 0.0979 time to fit residues: 39.0935 Evaluate side-chains 277 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 355 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 140 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 38 optimal weight: 0.1980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.084661 restraints weight = 16536.712| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.66 r_work: 0.2753 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11596 Z= 0.112 Angle : 0.510 8.234 15881 Z= 0.252 Chirality : 0.046 0.154 1783 Planarity : 0.005 0.048 2112 Dihedral : 4.338 20.222 1546 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.76 % Allowed : 13.81 % Favored : 84.44 % 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: -1.55 (0.21), residues: 1457 helix: -2.32 (0.46), residues: 79 sheet: -0.51 (0.25), residues: 389 loop : -1.17 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 290 TYR 0.014 0.001 TYR A 314 PHE 0.015 0.001 PHE C 83 TRP 0.008 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00276 (11596) covalent geometry : angle 0.51018 (15881) hydrogen bonds : bond 0.02931 ( 246) hydrogen bonds : angle 5.42957 ( 624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 57 TRP cc_start: 0.9075 (m100) cc_final: 0.8812 (m100) REVERT: B 192 ARG cc_start: 0.8336 (mmt-90) cc_final: 0.7462 (mtt180) REVERT: B 231 GLN cc_start: 0.8367 (tt0) cc_final: 0.8072 (tt0) REVERT: B 422 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7809 (t80) REVERT: A 80 ASP cc_start: 0.8576 (m-30) cc_final: 0.8353 (m-30) REVERT: A 396 ASP cc_start: 0.8915 (t0) cc_final: 0.8702 (t0) REVERT: C 231 GLN cc_start: 0.8376 (pt0) cc_final: 0.8156 (pt0) REVERT: C 287 GLN cc_start: 0.9105 (mt0) cc_final: 0.8803 (mt0) REVERT: C 349 MET cc_start: 0.8650 (mmm) cc_final: 0.8395 (mmm) outliers start: 22 outliers final: 16 residues processed: 281 average time/residue: 0.1044 time to fit residues: 42.5122 Evaluate side-chains 279 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 2 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 117 optimal weight: 0.0470 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN A 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.109807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.084929 restraints weight = 16571.333| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.66 r_work: 0.2801 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11596 Z= 0.118 Angle : 0.512 8.414 15881 Z= 0.250 Chirality : 0.046 0.153 1783 Planarity : 0.005 0.045 2112 Dihedral : 4.230 19.418 1546 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.15 % Allowed : 14.21 % Favored : 83.64 % 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: -1.34 (0.21), residues: 1457 helix: -2.05 (0.48), residues: 79 sheet: -0.47 (0.25), residues: 402 loop : -0.98 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 290 TYR 0.011 0.001 TYR A 314 PHE 0.015 0.001 PHE C 83 TRP 0.007 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00293 (11596) covalent geometry : angle 0.51173 (15881) hydrogen bonds : bond 0.02825 ( 246) hydrogen bonds : angle 5.29159 ( 624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 57 TRP cc_start: 0.9065 (m100) cc_final: 0.8798 (m100) REVERT: B 192 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7460 (mtt180) REVERT: B 231 GLN cc_start: 0.8353 (tt0) cc_final: 0.8051 (tt0) REVERT: B 422 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7794 (t80) REVERT: A 80 ASP cc_start: 0.8578 (m-30) cc_final: 0.8331 (m-30) REVERT: A 146 MET cc_start: 0.9312 (mtt) cc_final: 0.9109 (mtt) REVERT: A 181 MET cc_start: 0.9004 (mmm) cc_final: 0.8756 (mmm) REVERT: A 396 ASP cc_start: 0.8910 (t0) cc_final: 0.8707 (t0) REVERT: C 287 GLN cc_start: 0.9100 (mt0) cc_final: 0.8822 (mt0) REVERT: C 302 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7624 (tppt) REVERT: C 349 MET cc_start: 0.8648 (mmm) cc_final: 0.8401 (mmm) outliers start: 27 outliers final: 22 residues processed: 279 average time/residue: 0.1009 time to fit residues: 41.0232 Evaluate side-chains 284 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 144 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 chunk 58 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 5 optimal weight: 0.3980 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088089 restraints weight = 16382.503| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.64 r_work: 0.2583 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11596 Z= 0.146 Angle : 0.524 8.624 15881 Z= 0.256 Chirality : 0.046 0.153 1783 Planarity : 0.005 0.044 2112 Dihedral : 4.240 19.205 1546 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.55 % Allowed : 14.68 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.21), residues: 1457 helix: -1.86 (0.49), residues: 79 sheet: -0.39 (0.25), residues: 399 loop : -0.91 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 290 TYR 0.009 0.001 TYR A 314 PHE 0.015 0.001 PHE C 83 TRP 0.007 0.001 TRP C 385 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00364 (11596) covalent geometry : angle 0.52399 (15881) hydrogen bonds : bond 0.02936 ( 246) hydrogen bonds : angle 5.22303 ( 624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 0.423 Fit side-chains REVERT: B 57 TRP cc_start: 0.9042 (m100) cc_final: 0.8755 (m100) REVERT: B 192 ARG cc_start: 0.8234 (mmt-90) cc_final: 0.7319 (mtt180) REVERT: B 231 GLN cc_start: 0.8290 (tt0) cc_final: 0.7957 (tt0) REVERT: B 422 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7834 (t80) REVERT: A 396 ASP cc_start: 0.8961 (t0) cc_final: 0.8686 (t0) REVERT: A 518 ARG cc_start: 0.8559 (ptp-110) cc_final: 0.7720 (ptm-80) REVERT: C 231 GLN cc_start: 0.8484 (pt0) cc_final: 0.8273 (pt0) REVERT: C 302 LYS cc_start: 0.7822 (ttmm) cc_final: 0.7496 (tppt) REVERT: C 349 MET cc_start: 0.8610 (mmm) cc_final: 0.8340 (mmm) outliers start: 32 outliers final: 24 residues processed: 276 average time/residue: 0.1014 time to fit residues: 40.6777 Evaluate side-chains 280 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 0.0670 chunk 137 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.087477 restraints weight = 16426.071| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.63 r_work: 0.2745 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11596 Z= 0.180 Angle : 0.545 8.181 15881 Z= 0.266 Chirality : 0.047 0.152 1783 Planarity : 0.005 0.044 2112 Dihedral : 4.315 19.261 1546 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.55 % Allowed : 14.68 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.21), residues: 1457 helix: -1.76 (0.50), residues: 79 sheet: -0.32 (0.26), residues: 390 loop : -0.86 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.008 0.001 TYR A 314 PHE 0.015 0.001 PHE C 83 TRP 0.007 0.001 TRP C 385 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00446 (11596) covalent geometry : angle 0.54538 (15881) hydrogen bonds : bond 0.03104 ( 246) hydrogen bonds : angle 5.22861 ( 624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.420 Fit side-chains REVERT: B 57 TRP cc_start: 0.9084 (m100) cc_final: 0.8816 (m100) REVERT: B 192 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.7514 (mtt180) REVERT: B 231 GLN cc_start: 0.8323 (tt0) cc_final: 0.8021 (tt0) REVERT: B 422 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 518 ARG cc_start: 0.8604 (ptp-110) cc_final: 0.7860 (ptm-80) REVERT: C 302 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7523 (tppt) REVERT: C 349 MET cc_start: 0.8631 (mmm) cc_final: 0.8359 (mmm) outliers start: 32 outliers final: 27 residues processed: 270 average time/residue: 0.1005 time to fit residues: 39.3059 Evaluate side-chains 283 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 135 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 127 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 HIS ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN C 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.082221 restraints weight = 16641.551| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.64 r_work: 0.2591 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11596 Z= 0.105 Angle : 0.520 9.134 15881 Z= 0.253 Chirality : 0.046 0.151 1783 Planarity : 0.005 0.043 2112 Dihedral : 4.173 18.768 1546 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.00 % Allowed : 15.48 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.00 (0.21), residues: 1457 helix: -1.42 (0.52), residues: 79 sheet: -0.23 (0.26), residues: 392 loop : -0.78 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.009 0.001 TYR A 314 PHE 0.015 0.001 PHE A 172 TRP 0.008 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00263 (11596) covalent geometry : angle 0.51996 (15881) hydrogen bonds : bond 0.02721 ( 246) hydrogen bonds : angle 5.08041 ( 624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 0.403 Fit side-chains REVERT: B 57 TRP cc_start: 0.9053 (m100) cc_final: 0.8768 (m100) REVERT: B 192 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7337 (mtt180) REVERT: B 231 GLN cc_start: 0.8235 (tt0) cc_final: 0.7880 (tt0) REVERT: B 422 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 80 ASP cc_start: 0.8349 (m-30) cc_final: 0.8097 (m-30) REVERT: A 181 MET cc_start: 0.9053 (mmm) cc_final: 0.8788 (mmm) REVERT: A 518 ARG cc_start: 0.8549 (ptp-110) cc_final: 0.7769 (ptm-80) REVERT: C 302 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7505 (tppt) REVERT: C 349 MET cc_start: 0.8605 (mmm) cc_final: 0.8339 (mmm) outliers start: 25 outliers final: 22 residues processed: 273 average time/residue: 0.1036 time to fit residues: 40.8628 Evaluate side-chains 281 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 26 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.090424 restraints weight = 16313.467| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.58 r_work: 0.2776 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11596 Z= 0.118 Angle : 0.518 8.069 15881 Z= 0.252 Chirality : 0.046 0.152 1783 Planarity : 0.005 0.044 2112 Dihedral : 4.105 18.237 1546 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.08 % Allowed : 15.40 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.87 (0.21), residues: 1457 helix: -1.24 (0.53), residues: 79 sheet: -0.23 (0.26), residues: 391 loop : -0.65 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.010 0.001 TYR C 520 PHE 0.014 0.001 PHE A 172 TRP 0.007 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00295 (11596) covalent geometry : angle 0.51795 (15881) hydrogen bonds : bond 0.02725 ( 246) hydrogen bonds : angle 5.02380 ( 624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 57 TRP cc_start: 0.9069 (m100) cc_final: 0.8817 (m100) REVERT: B 192 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.7597 (mtt180) REVERT: B 231 GLN cc_start: 0.8341 (tt0) cc_final: 0.8028 (tt0) REVERT: B 374 ASP cc_start: 0.8422 (t70) cc_final: 0.7530 (p0) REVERT: B 422 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7858 (t80) REVERT: A 181 MET cc_start: 0.9008 (mmm) cc_final: 0.8778 (mmm) REVERT: C 246 ARG cc_start: 0.8809 (mtm180) cc_final: 0.8601 (mtm-85) REVERT: C 302 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7656 (tppt) REVERT: C 349 MET cc_start: 0.8614 (mmm) cc_final: 0.8399 (mmm) outliers start: 26 outliers final: 23 residues processed: 272 average time/residue: 0.1032 time to fit residues: 40.4855 Evaluate side-chains 281 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 210 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 95 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN ** B 356 GLN ** 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 = 0.3205 r_free = 0.3205 target = 0.111505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.087117 restraints weight = 16260.373| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.58 r_work: 0.2661 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 11596 Z= 0.213 Angle : 0.803 59.182 15881 Z= 0.464 Chirality : 0.046 0.151 1783 Planarity : 0.005 0.044 2112 Dihedral : 4.141 22.740 1546 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.00 % Allowed : 15.00 % Favored : 83.00 % Cbeta Deviations : 0.07 % 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: -0.86 (0.21), residues: 1457 helix: -1.23 (0.53), residues: 79 sheet: -0.22 (0.26), residues: 391 loop : -0.65 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.009 0.001 TYR C 520 PHE 0.014 0.001 PHE A 172 TRP 0.007 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00418 (11596) covalent geometry : angle 0.80271 (15881) hydrogen bonds : bond 0.02744 ( 246) hydrogen bonds : angle 5.02433 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.66 seconds wall clock time: 46 minutes 52.58 seconds (2812.58 seconds total)