Starting phenix.real_space_refine on Fri Sep 11 00:26:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6g79_4358/09_2026/6g79_4358.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g79_4358/09_2026/6g79_4358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6g79_4358/09_2026/6g79_4358.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6g79_4358/09_2026/6g79_4358.cif" model { file = "/net/cci-nas-00/data/ceres_data/6g79_4358/09_2026/6g79_4358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g79_4358/09_2026/6g79_4358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6g79_4358/09_2026/6g79_4358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g79_4358/09_2026/6g79_4358.map" } resolution = 3.78 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= 0.002 sd= 0.016 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 34 5.16 5 C 3922 2.51 5 N 1021 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6053 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2270 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 23, 'GLN:plan1': 7, 'ARG:plan': 14, 'ASN:plan1': 7, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 226 Chain: "G" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 342 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1448 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 6, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 130 Chain: "S" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1963 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 251} Chain breaks: 3 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "S" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'EP5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.24 Number of scatterers: 6053 At special positions: 0 Unit cell: (94.34, 109.18, 97.52, 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 34 16.00 O 1076 8.00 N 1021 7.00 C 3922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 122 " - pdb=" SG CYS S 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 372.5 milliseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1634 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 48.8% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.600A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.819A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.325A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 214' Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 230 through 256 removed outlier: 3.593A pdb=" N LEU A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.062A pdb=" N ASP A 262 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.717A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 331 through 352 Processing helix chain 'S' and resid 46 through 77 Processing helix chain 'S' and resid 82 through 102 removed outlier: 3.846A pdb=" N LEU S 87 " --> pdb=" O PRO S 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE S 88 " --> pdb=" O ALA S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 113 removed outlier: 3.967A pdb=" N MET S 108 " --> pdb=" O PRO S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 153 removed outlier: 4.250A pdb=" N VAL S 121 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER S 127 " --> pdb=" O ASP S 123 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU S 140 " --> pdb=" O SER S 136 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS S 141 " --> pdb=" O ILE S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 154 through 161 removed outlier: 4.201A pdb=" N ALA S 159 " --> pdb=" O VAL S 155 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS S 160 " --> pdb=" O GLU S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 162 through 182 Processing helix chain 'S' and resid 205 through 216 Processing helix chain 'S' and resid 217 through 240 Processing helix chain 'S' and resid 306 through 337 removed outlier: 3.808A pdb=" N PHE S 323 " --> pdb=" O ILE S 319 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS S 326 " --> pdb=" O ALA S 322 " (cutoff:3.500A) Proline residue: S 329 - end of helix removed outlier: 3.807A pdb=" N LEU S 335 " --> pdb=" O PHE S 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 373 removed outlier: 3.628A pdb=" N TRP S 356 " --> pdb=" O ASP S 352 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER S 362 " --> pdb=" O GLY S 358 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU S 363 " --> pdb=" O TYR S 359 " (cutoff:3.500A) Proline residue: S 366 - end of helix removed outlier: 4.027A pdb=" N ASN S 373 " --> pdb=" O TYR S 369 " (cutoff:3.500A) Processing helix chain 'S' and resid 373 through 384 removed outlier: 3.607A pdb=" N HIS S 381 " --> pdb=" O LYS S 377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.585A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.963A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.500A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.043A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.697A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 233 through 234 removed outlier: 3.627A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.336A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 197 through 200 removed outlier: 3.859A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1080 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: 1.00 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 943 1.29 - 1.42: 1667 1.42 - 1.55: 3482 1.55 - 1.68: 53 1.68 - 1.81: 42 Bond restraints: 6187 Sorted by residual: bond pdb=" C10 EP5 S 401 " pdb=" C7 EP5 S 401 " ideal model delta sigma weight residual 1.421 1.284 0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C15 EP5 S 401 " pdb=" C16 EP5 S 401 " ideal model delta sigma weight residual 1.412 1.476 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" N TYR A 231 " pdb=" CA TYR A 231 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.64e+00 bond pdb=" CA PRO S 183 " pdb=" C PRO S 183 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.21e+00 bond pdb=" C15 EP5 S 401 " pdb=" C20 EP5 S 401 " ideal model delta sigma weight residual 1.432 1.480 -0.048 2.00e-02 2.50e+03 5.74e+00 ... (remaining 6182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 7410 1.70 - 3.40: 990 3.40 - 5.10: 73 5.10 - 6.80: 15 6.80 - 8.49: 3 Bond angle restraints: 8491 Sorted by residual: angle pdb=" N TYR A 231 " pdb=" CA TYR A 231 " pdb=" C TYR A 231 " ideal model delta sigma weight residual 112.90 119.49 -6.59 1.31e+00 5.83e-01 2.53e+01 angle pdb=" N PRO S 183 " pdb=" CA PRO S 183 " pdb=" C PRO S 183 " ideal model delta sigma weight residual 110.70 116.78 -6.08 1.22e+00 6.72e-01 2.48e+01 angle pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sigma weight residual 113.90 105.57 8.33 1.80e+00 3.09e-01 2.14e+01 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 110.72 115.01 -4.29 1.01e+00 9.80e-01 1.81e+01 angle pdb=" N ASN A 242 " pdb=" CA ASN A 242 " pdb=" C ASN A 242 " ideal model delta sigma weight residual 111.28 106.88 4.40 1.09e+00 8.42e-01 1.63e+01 ... (remaining 8486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 3291 16.39 - 32.77: 191 32.77 - 49.15: 50 49.15 - 65.54: 8 65.54 - 81.92: 2 Dihedral angle restraints: 3542 sinusoidal: 1034 harmonic: 2508 Sorted by residual: dihedral pdb=" C TYR A 231 " pdb=" N TYR A 231 " pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " ideal model delta harmonic sigma weight residual -122.60 -130.65 8.05 0 2.50e+00 1.60e-01 1.04e+01 dihedral pdb=" CA HIS S 347 " pdb=" C HIS S 347 " pdb=" N LEU S 348 " pdb=" CA LEU S 348 " ideal model delta harmonic sigma weight residual -180.00 -164.47 -15.53 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" CA ARG S 308 " pdb=" CB ARG S 308 " pdb=" CG ARG S 308 " pdb=" CD ARG S 308 " ideal model delta sinusoidal sigma weight residual -180.00 -124.25 -55.75 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 3539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 859 0.075 - 0.150: 162 0.150 - 0.225: 30 0.225 - 0.300: 1 0.300 - 0.375: 1 Chirality restraints: 1053 Sorted by residual: chirality pdb=" CA TYR A 231 " pdb=" N TYR A 231 " pdb=" C TYR A 231 " pdb=" CB TYR A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1050 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N EP5 S 401 " 0.004 2.00e-02 2.50e+03 9.37e-02 1.32e+02 pdb=" O EP5 S 401 " -0.120 2.00e-02 2.50e+03 pdb=" C1 EP5 S 401 " 0.117 2.00e-02 2.50e+03 pdb=" C11 EP5 S 401 " -0.007 2.00e-02 2.50e+03 pdb=" C12 EP5 S 401 " 0.114 2.00e-02 2.50e+03 pdb=" C2 EP5 S 401 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 231 " 0.029 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR A 231 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 231 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 231 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 231 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 231 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE S 219 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO S 220 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO S 220 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 220 " 0.035 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 2390 2.93 - 3.43: 6086 3.43 - 3.92: 9935 3.92 - 4.41: 11024 4.41 - 4.90: 19046 Nonbonded interactions: 48481 Sorted by model distance: nonbonded pdb=" O ARG A 243 " pdb=" OG SER A 247 " model vdw 2.442 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.553 3.040 nonbonded pdb=" O PRO S 366 " pdb=" OG1 THR S 370 " model vdw 2.559 3.040 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.561 3.040 nonbonded pdb=" O ILE S 130 " pdb=" OG1 THR S 134 " model vdw 2.564 3.040 ... (remaining 48476 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.330 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.470 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.008 0.137 6188 Z= 0.537 Angle : 1.152 8.494 8493 Z= 0.779 Chirality : 0.060 0.375 1053 Planarity : 0.005 0.094 1051 Dihedral : 12.120 81.922 1905 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.88 % Favored : 94.64 % Rotamer: Outliers : 0.56 % Allowed : 6.15 % Favored : 93.30 % 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: -2.95 (0.24), residues: 840 helix: -0.61 (0.22), residues: 360 sheet: -3.35 (0.27), residues: 164 loop : -2.61 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.046 0.002 TYR A 231 PHE 0.015 0.002 PHE A 190 TRP 0.010 0.001 TRP S 149 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.54 ( 6187) covalent geometry : angle 1.15258 / 0.78 ( 8491) SS BOND : bond 0.00131 / 0.07 ( 1) SS BOND : angle 0.37986 / 0.21 ( 2) hydrogen bonds : bond 0.24993 / 18.26 ( 368) hydrogen bonds : angle 8.96211 / 6.35 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 188 MET cc_start: 0.7993 (mmm) cc_final: 0.7060 (mmm) REVERT: B 323 ASP cc_start: 0.8728 (p0) cc_final: 0.8515 (p0) REVERT: B 339 TRP cc_start: 0.8405 (m100) cc_final: 0.8087 (m100) REVERT: G 18 GLN cc_start: 0.9014 (tp40) cc_final: 0.8552 (tp-100) REVERT: A 244 MET cc_start: 0.8375 (tpp) cc_final: 0.7516 (mmt) REVERT: A 305 GLN cc_start: 0.8798 (tt0) cc_final: 0.7820 (tm-30) REVERT: A 312 ASN cc_start: 0.8860 (t0) cc_final: 0.8527 (t0) REVERT: S 169 MET cc_start: 0.8507 (mmm) cc_final: 0.8016 (mmp) REVERT: S 205 HIS cc_start: 0.7891 (m170) cc_final: 0.7681 (m-70) REVERT: S 313 THR cc_start: 0.9124 (m) cc_final: 0.8916 (p) outliers start: 3 outliers final: 1 residues processed: 191 average time/residue: 0.0572 time to fit residues: 15.3096 Evaluate side-chains 115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 333 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 230 ASN B 295 ASN G 18 GLN A 307 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111169 restraints weight = 11372.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114162 restraints weight = 6487.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116289 restraints weight = 4542.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117715 restraints weight = 3550.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118432 restraints weight = 2996.431| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6188 Z= 0.140 Angle : 0.630 16.448 8493 Z= 0.318 Chirality : 0.041 0.197 1053 Planarity : 0.005 0.077 1051 Dihedral : 6.041 76.818 905 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.79 % Favored : 97.98 % Rotamer: Outliers : 3.72 % Allowed : 14.53 % Favored : 81.75 % 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: -0.97 (0.28), residues: 840 helix: 1.48 (0.25), residues: 375 sheet: -2.50 (0.32), residues: 172 loop : -2.26 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 15 TYR 0.013 0.002 TYR B 264 PHE 0.011 0.002 PHE S 331 TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 6187) covalent geometry : angle 0.62980 / 0.32 ( 8491) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 0.61794 / 0.34 ( 2) hydrogen bonds : bond 0.04903 / 3.62 ( 368) hydrogen bonds : angle 4.84636 / 3.45 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.194 Fit side-chains REVERT: B 188 MET cc_start: 0.8040 (mmm) cc_final: 0.7621 (mmm) REVERT: B 243 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8323 (p) REVERT: B 262 MET cc_start: 0.7725 (tpp) cc_final: 0.7393 (mmm) REVERT: B 277 SER cc_start: 0.8485 (t) cc_final: 0.8106 (t) REVERT: B 339 TRP cc_start: 0.8483 (m100) cc_final: 0.7999 (m100) REVERT: G 40 TYR cc_start: 0.8482 (t80) cc_final: 0.8195 (t80) REVERT: A 25 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7782 (tp30) REVERT: A 244 MET cc_start: 0.8081 (tpp) cc_final: 0.7676 (mmt) REVERT: A 305 GLN cc_start: 0.8482 (tt0) cc_final: 0.7890 (tm-30) REVERT: A 313 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7100 (ptt90) REVERT: S 55 LEU cc_start: 0.9036 (tt) cc_final: 0.8796 (tp) REVERT: S 367 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (pt) outliers start: 20 outliers final: 11 residues processed: 145 average time/residue: 0.0588 time to fit residues: 12.0240 Evaluate side-chains 123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 231 ILE Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 52 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 18 GLN S 202 ASN S 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104688 restraints weight = 11572.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107442 restraints weight = 6808.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109340 restraints weight = 4835.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110525 restraints weight = 3833.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111458 restraints weight = 3298.538| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6188 Z= 0.206 Angle : 0.642 16.192 8493 Z= 0.324 Chirality : 0.043 0.177 1053 Planarity : 0.005 0.079 1051 Dihedral : 5.814 78.335 905 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.86 % Favored : 96.90 % Rotamer: Outliers : 4.84 % Allowed : 16.57 % Favored : 78.58 % 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: -0.21 (0.29), residues: 840 helix: 2.08 (0.25), residues: 376 sheet: -2.05 (0.33), residues: 180 loop : -1.88 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 15 TYR 0.012 0.002 TYR B 264 PHE 0.031 0.002 PHE B 253 TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 ( 6187) covalent geometry : angle 0.64168 / 0.32 ( 8491) SS BOND : bond 0.00227 / 0.12 ( 1) SS BOND : angle 0.41728 / 0.24 ( 2) hydrogen bonds : bond 0.04141 / 3.04 ( 368) hydrogen bonds : angle 4.52204 / 3.23 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.166 Fit side-chains REVERT: B 188 MET cc_start: 0.8161 (mmm) cc_final: 0.7954 (mmm) REVERT: B 339 TRP cc_start: 0.8759 (m100) cc_final: 0.8319 (m100) REVERT: A 305 GLN cc_start: 0.8382 (tt0) cc_final: 0.8021 (tm-30) REVERT: S 148 TYR cc_start: 0.8208 (t80) cc_final: 0.7828 (t80) REVERT: S 157 TYR cc_start: 0.8564 (t80) cc_final: 0.8363 (t80) outliers start: 26 outliers final: 14 residues processed: 142 average time/residue: 0.0547 time to fit residues: 11.1142 Evaluate side-chains 116 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 178 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109719 restraints weight = 11314.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112668 restraints weight = 6624.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114672 restraints weight = 4690.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115808 restraints weight = 3702.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116677 restraints weight = 3184.223| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6188 Z= 0.142 Angle : 0.601 16.243 8493 Z= 0.294 Chirality : 0.040 0.166 1053 Planarity : 0.005 0.084 1051 Dihedral : 5.528 75.913 905 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.26 % Favored : 97.50 % Rotamer: Outliers : 4.47 % Allowed : 19.18 % Favored : 76.35 % 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 (0.29), residues: 840 helix: 2.25 (0.25), residues: 378 sheet: -1.82 (0.33), residues: 184 loop : -1.61 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 15 TYR 0.019 0.002 TYR B 289 PHE 0.030 0.002 PHE B 253 TRP 0.015 0.002 TRP S 356 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6187) covalent geometry : angle 0.60121 / 0.29 ( 8491) SS BOND : bond 0.00176 / 0.09 ( 1) SS BOND : angle 0.34159 / 0.18 ( 2) hydrogen bonds : bond 0.03644 / 2.68 ( 368) hydrogen bonds : angle 4.36625 / 3.12 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.294 Fit side-chains REVERT: B 150 ARG cc_start: 0.8641 (mmt90) cc_final: 0.8404 (mmt-90) REVERT: B 188 MET cc_start: 0.8215 (mmm) cc_final: 0.7990 (mmm) REVERT: A 305 GLN cc_start: 0.8313 (tt0) cc_final: 0.7935 (tm-30) REVERT: A 313 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7001 (ptp90) REVERT: S 55 LEU cc_start: 0.9008 (tt) cc_final: 0.8801 (tp) REVERT: S 126 LEU cc_start: 0.8775 (mt) cc_final: 0.8508 (mt) REVERT: S 148 TYR cc_start: 0.8181 (t80) cc_final: 0.7853 (t80) REVERT: S 157 TYR cc_start: 0.8524 (t80) cc_final: 0.8313 (t80) outliers start: 24 outliers final: 14 residues processed: 127 average time/residue: 0.0627 time to fit residues: 10.9109 Evaluate side-chains 119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 50.0000 chunk 9 optimal weight: 0.0060 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109149 restraints weight = 11417.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.112174 restraints weight = 6584.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114191 restraints weight = 4596.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115400 restraints weight = 3605.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116410 restraints weight = 3104.140| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6188 Z= 0.146 Angle : 0.584 16.172 8493 Z= 0.288 Chirality : 0.040 0.171 1053 Planarity : 0.005 0.087 1051 Dihedral : 5.402 74.464 905 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.98 % Favored : 96.79 % Rotamer: Outliers : 3.72 % Allowed : 20.48 % Favored : 75.79 % 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: 0.35 (0.29), residues: 840 helix: 2.33 (0.25), residues: 384 sheet: -1.54 (0.35), residues: 173 loop : -1.55 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 15 TYR 0.012 0.001 TYR B 289 PHE 0.014 0.001 PHE B 199 TRP 0.015 0.002 TRP S 356 HIS 0.006 0.001 HIS S 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 6187) covalent geometry : angle 0.58380 / 0.29 ( 8491) SS BOND : bond 0.00167 / 0.09 ( 1) SS BOND : angle 0.29350 / 0.16 ( 2) hydrogen bonds : bond 0.03529 / 2.59 ( 368) hydrogen bonds : angle 4.32983 / 3.09 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.216 Fit side-chains REVERT: B 150 ARG cc_start: 0.8659 (mmt90) cc_final: 0.8393 (mmt-90) REVERT: B 188 MET cc_start: 0.8174 (mmm) cc_final: 0.7934 (mmm) REVERT: A 305 GLN cc_start: 0.8309 (tt0) cc_final: 0.7652 (tm-30) REVERT: A 313 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6999 (ptp90) REVERT: S 148 TYR cc_start: 0.8219 (t80) cc_final: 0.7933 (t80) REVERT: S 218 TYR cc_start: 0.7709 (m-80) cc_final: 0.7355 (m-80) outliers start: 20 outliers final: 14 residues processed: 123 average time/residue: 0.0600 time to fit residues: 10.2146 Evaluate side-chains 120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 18 GLN S 202 ASN S 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111975 restraints weight = 11208.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115021 restraints weight = 6443.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117108 restraints weight = 4498.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118082 restraints weight = 3500.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119329 restraints weight = 3052.191| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6188 Z= 0.112 Angle : 0.554 15.942 8493 Z= 0.272 Chirality : 0.039 0.182 1053 Planarity : 0.005 0.088 1051 Dihedral : 5.242 74.769 905 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.26 % Favored : 97.50 % Rotamer: Outliers : 3.72 % Allowed : 21.04 % Favored : 75.23 % 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: 0.63 (0.29), residues: 840 helix: 2.55 (0.25), residues: 380 sheet: -1.18 (0.37), residues: 171 loop : -1.51 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.009 0.001 TYR B 59 PHE 0.013 0.001 PHE B 199 TRP 0.014 0.001 TRP S 356 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6187) covalent geometry : angle 0.55428 / 0.27 ( 8491) SS BOND : bond 0.00160 / 0.08 ( 1) SS BOND : angle 0.08639 / 0.05 ( 2) hydrogen bonds : bond 0.03229 / 2.38 ( 368) hydrogen bonds : angle 4.19828 / 2.98 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.221 Fit side-chains REVERT: B 58 ILE cc_start: 0.8651 (mt) cc_final: 0.8241 (tt) REVERT: B 150 ARG cc_start: 0.8588 (mmt90) cc_final: 0.8310 (mmt-90) REVERT: A 305 GLN cc_start: 0.8309 (tt0) cc_final: 0.7572 (tm-30) REVERT: A 313 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6937 (ptp90) REVERT: S 359 TYR cc_start: 0.8723 (m-10) cc_final: 0.8429 (m-10) outliers start: 20 outliers final: 13 residues processed: 133 average time/residue: 0.0679 time to fit residues: 12.4912 Evaluate side-chains 128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 50.0000 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 0.0270 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 overall best weight: 1.2640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111826 restraints weight = 11330.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114946 restraints weight = 6496.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.116987 restraints weight = 4517.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118261 restraints weight = 3537.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119215 restraints weight = 3026.256| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6188 Z= 0.120 Angle : 0.554 15.741 8493 Z= 0.275 Chirality : 0.039 0.166 1053 Planarity : 0.005 0.088 1051 Dihedral : 5.234 75.103 905 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.62 % Favored : 97.14 % Rotamer: Outliers : 3.17 % Allowed : 23.65 % Favored : 73.18 % 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: 0.76 (0.30), residues: 840 helix: 2.55 (0.25), residues: 386 sheet: -1.12 (0.37), residues: 173 loop : -1.37 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.013 0.001 TYR S 157 PHE 0.014 0.001 PHE S 176 TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6187) covalent geometry : angle 0.55397 / 0.28 ( 8491) SS BOND : bond 0.00138 / 0.07 ( 1) SS BOND : angle 0.14585 / 0.08 ( 2) hydrogen bonds : bond 0.03204 / 2.36 ( 368) hydrogen bonds : angle 4.15127 / 2.96 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.223 Fit side-chains REVERT: B 58 ILE cc_start: 0.8703 (mt) cc_final: 0.8265 (tt) REVERT: A 244 MET cc_start: 0.7570 (tpp) cc_final: 0.7300 (tmm) REVERT: A 305 GLN cc_start: 0.8280 (tt0) cc_final: 0.7548 (tm-30) REVERT: A 313 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6957 (ptp90) REVERT: S 218 TYR cc_start: 0.7669 (m-80) cc_final: 0.7365 (m-80) REVERT: S 359 TYR cc_start: 0.8749 (m-10) cc_final: 0.8512 (m-10) outliers start: 17 outliers final: 14 residues processed: 124 average time/residue: 0.0583 time to fit residues: 10.0183 Evaluate side-chains 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.133242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113798 restraints weight = 11065.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116864 restraints weight = 6354.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118957 restraints weight = 4427.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120154 restraints weight = 3458.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121066 restraints weight = 2963.085| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6188 Z= 0.104 Angle : 0.548 15.355 8493 Z= 0.269 Chirality : 0.038 0.151 1053 Planarity : 0.005 0.092 1051 Dihedral : 5.208 78.439 905 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.14 % Favored : 97.62 % Rotamer: Outliers : 2.79 % Allowed : 23.28 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.30), residues: 840 helix: 2.68 (0.25), residues: 386 sheet: -0.97 (0.38), residues: 171 loop : -1.28 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 15 TYR 0.012 0.001 TYR S 157 PHE 0.013 0.001 PHE S 176 TRP 0.013 0.001 TRP S 356 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 6187) covalent geometry : angle 0.54767 / 0.27 ( 8491) SS BOND : bond 0.00138 / 0.07 ( 1) SS BOND : angle 0.10974 / 0.06 ( 2) hydrogen bonds : bond 0.03031 / 2.25 ( 368) hydrogen bonds : angle 4.04704 / 2.89 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.218 Fit side-chains REVERT: B 58 ILE cc_start: 0.8666 (mt) cc_final: 0.8248 (tt) REVERT: A 305 GLN cc_start: 0.8287 (tt0) cc_final: 0.7486 (tm-30) REVERT: A 313 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6947 (ptp90) REVERT: S 55 LEU cc_start: 0.9090 (tt) cc_final: 0.8860 (tp) REVERT: S 218 TYR cc_start: 0.7641 (m-80) cc_final: 0.7338 (m-80) REVERT: S 359 TYR cc_start: 0.8737 (m-10) cc_final: 0.8528 (m-10) outliers start: 15 outliers final: 14 residues processed: 126 average time/residue: 0.0615 time to fit residues: 10.9992 Evaluate side-chains 129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114201 restraints weight = 11211.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117252 restraints weight = 6438.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119356 restraints weight = 4485.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120680 restraints weight = 3511.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121628 restraints weight = 2972.608| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6188 Z= 0.106 Angle : 0.560 14.952 8493 Z= 0.276 Chirality : 0.038 0.141 1053 Planarity : 0.005 0.091 1051 Dihedral : 4.999 78.271 903 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.02 % Favored : 97.74 % Rotamer: Outliers : 3.54 % Allowed : 23.65 % Favored : 72.81 % 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: 1.06 (0.30), residues: 840 helix: 2.85 (0.25), residues: 380 sheet: -0.86 (0.39), residues: 169 loop : -1.30 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 15 TYR 0.019 0.001 TYR B 85 PHE 0.020 0.001 PHE B 222 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 6187) covalent geometry : angle 0.56006 / 0.28 ( 8491) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.11468 / 0.06 ( 2) hydrogen bonds : bond 0.03033 / 2.25 ( 368) hydrogen bonds : angle 3.99575 / 2.86 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.188 Fit side-chains REVERT: B 58 ILE cc_start: 0.8631 (mt) cc_final: 0.8261 (tt) REVERT: B 105 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7985 (t80) REVERT: A 244 MET cc_start: 0.7553 (tmm) cc_final: 0.6762 (mmt) REVERT: A 305 GLN cc_start: 0.8320 (tt0) cc_final: 0.7462 (tm-30) REVERT: A 313 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6844 (ptp90) REVERT: S 55 LEU cc_start: 0.8983 (tt) cc_final: 0.8743 (tp) REVERT: S 238 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.8002 (tpp-160) REVERT: S 346 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.5346 (t80) REVERT: S 359 TYR cc_start: 0.8748 (m-10) cc_final: 0.8535 (m-10) outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 0.0573 time to fit residues: 9.8449 Evaluate side-chains 128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 346 PHE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.133940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114421 restraints weight = 11245.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117525 restraints weight = 6456.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119605 restraints weight = 4483.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121007 restraints weight = 3516.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121660 restraints weight = 2968.955| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6188 Z= 0.110 Angle : 0.573 14.449 8493 Z= 0.283 Chirality : 0.038 0.136 1053 Planarity : 0.005 0.092 1051 Dihedral : 4.991 77.937 903 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.50 % Favored : 97.38 % Rotamer: Outliers : 3.17 % Allowed : 24.02 % Favored : 72.81 % 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: 1.10 (0.30), residues: 840 helix: 2.85 (0.25), residues: 381 sheet: -0.82 (0.39), residues: 171 loop : -1.25 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 15 TYR 0.013 0.001 TYR S 157 PHE 0.019 0.001 PHE A 275 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6187) covalent geometry : angle 0.57272 / 0.28 ( 8491) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.12584 / 0.07 ( 2) hydrogen bonds : bond 0.03000 / 2.22 ( 368) hydrogen bonds : angle 3.96947 / 2.84 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.226 Fit side-chains REVERT: B 58 ILE cc_start: 0.8675 (mt) cc_final: 0.8330 (tt) REVERT: B 105 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.8039 (t80) REVERT: B 339 TRP cc_start: 0.8895 (m100) cc_final: 0.8679 (m100) REVERT: A 244 MET cc_start: 0.7700 (tmm) cc_final: 0.7353 (tpp) REVERT: A 313 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6861 (ptp90) REVERT: S 55 LEU cc_start: 0.9000 (tt) cc_final: 0.8770 (tp) REVERT: S 346 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.5382 (t80) REVERT: S 359 TYR cc_start: 0.8754 (m-10) cc_final: 0.8537 (m-10) outliers start: 17 outliers final: 13 residues processed: 121 average time/residue: 0.0614 time to fit residues: 10.4026 Evaluate side-chains 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 346 PHE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.0470 chunk 75 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116006 restraints weight = 11270.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119108 restraints weight = 6424.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121219 restraints weight = 4436.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122642 restraints weight = 3460.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123475 restraints weight = 2903.380| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6188 Z= 0.102 Angle : 0.553 13.592 8493 Z= 0.274 Chirality : 0.038 0.168 1053 Planarity : 0.005 0.095 1051 Dihedral : 4.903 77.739 903 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.26 % Favored : 97.62 % Rotamer: Outliers : 2.79 % Allowed : 24.77 % Favored : 72.44 % 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: 1.17 (0.30), residues: 840 helix: 2.89 (0.25), residues: 382 sheet: -0.74 (0.39), residues: 171 loop : -1.25 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 15 TYR 0.013 0.001 TYR S 148 PHE 0.017 0.001 PHE B 222 TRP 0.012 0.001 TRP S 356 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 6187) covalent geometry : angle 0.55271 / 0.27 ( 8491) SS BOND : bond 0.00143 / 0.08 ( 1) SS BOND : angle 0.10235 / 0.06 ( 2) hydrogen bonds : bond 0.02930 / 2.18 ( 368) hydrogen bonds : angle 3.90009 / 2.78 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1060.16 seconds wall clock time: 19 minutes 4.83 seconds (1144.83 seconds total)