Starting phenix.real_space_refine on Thu Jul 2 05:59:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mby_23750/07_2026/7mby_23750.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mby_23750/07_2026/7mby_23750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2026/7mby_23750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2026/7mby_23750.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2026/7mby_23750.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2026/7mby_23750.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2026/7mby_23750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mby_23750/07_2026/7mby_23750.cif" } resolution = 2.44 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= 0.032 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 4416 2.51 5 N 1164 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6881 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2501 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 8, 'GLN:plan1': 2, 'ASN:plan1': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 407 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2250 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 4, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.22 Number of scatterers: 6881 At special positions: 0 Unit cell: (73.45, 102.7, 121.55, 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 1244 8.00 N 1164 7.00 C 4416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 347.2 milliseconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 47.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.561A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.614A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 39 through 69 removed outlier: 4.052A pdb=" N VAL R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 95 removed outlier: 3.838A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 105 Processing helix chain 'R' and resid 110 through 145 removed outlier: 3.511A pdb=" N GLY R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 removed outlier: 4.334A pdb=" N VAL R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP R 152 " --> pdb=" O GLN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'R' and resid 174 through 179 removed outlier: 4.270A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 218 removed outlier: 3.539A pdb=" N SER R 208 " --> pdb=" O VAL R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 238 removed outlier: 3.978A pdb=" N MET R 226 " --> pdb=" O GLY R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 339 removed outlier: 3.547A pdb=" N ARG R 313 " --> pdb=" O LYS R 309 " (cutoff:3.500A) Proline residue: R 328 - end of helix removed outlier: 3.644A pdb=" N TYR R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 347 removed outlier: 3.930A pdb=" N ALA R 343 " --> pdb=" O ASP R 339 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 361 Processing helix chain 'R' and resid 361 through 371 Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 removed outlier: 3.511A pdb=" N LEU R 379 " --> pdb=" O LYS R 375 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 39 removed outlier: 3.541A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 4.147A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.506A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.767A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.172A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.946A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.014A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.568A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.516A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.668A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.810A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.512A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 180 through 186 removed outlier: 3.599A pdb=" N ASN R 181 " --> pdb=" O ARG R 197 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG R 197 " --> pdb=" O ASN R 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.916A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 292 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1113 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: 1.08 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1095 1.31 - 1.44: 1909 1.44 - 1.56: 3926 1.56 - 1.69: 6 1.69 - 1.82: 84 Bond restraints: 7020 Sorted by residual: bond pdb=" CAI Y01 R 501 " pdb=" CAK Y01 R 501 " ideal model delta sigma weight residual 1.492 1.582 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" CAZ Y01 R 501 " pdb=" CBH Y01 R 501 " ideal model delta sigma weight residual 1.519 1.441 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CAK Y01 R 501 " pdb=" CBD Y01 R 501 " ideal model delta sigma weight residual 1.525 1.598 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CAP Y01 R 501 " pdb=" CAQ Y01 R 501 " ideal model delta sigma weight residual 1.541 1.610 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" CAY Y01 R 501 " pdb=" OAW Y01 R 501 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 7015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 9366 2.90 - 5.81: 147 5.81 - 8.71: 23 8.71 - 11.62: 4 11.62 - 14.52: 1 Bond angle restraints: 9541 Sorted by residual: angle pdb=" C ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta sigma weight residual 110.79 100.70 10.09 1.68e+00 3.54e-01 3.61e+01 angle pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 115.16 100.64 14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 125.66 132.89 -7.23 1.85e+00 2.92e-01 1.53e+01 angle pdb=" OH TYS P 2 " pdb=" S TYS P 2 " pdb=" O3 TYS P 2 " ideal model delta sigma weight residual 100.21 111.53 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CA GLY B 319 " pdb=" C GLY B 319 " pdb=" O GLY B 319 " ideal model delta sigma weight residual 121.19 117.83 3.36 9.10e-01 1.21e+00 1.36e+01 ... (remaining 9536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 3960 21.72 - 43.44: 168 43.44 - 65.15: 18 65.15 - 86.87: 2 86.87 - 108.59: 1 Dihedral angle restraints: 4149 sinusoidal: 1545 harmonic: 2604 Sorted by residual: dihedral pdb=" C ARG R 376 " pdb=" N ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta harmonic sigma weight residual -122.60 -108.99 -13.61 0 2.50e+00 1.60e-01 2.96e+01 dihedral pdb=" CBC Y01 R 501 " pdb=" CAR Y01 R 501 " pdb=" CAT Y01 R 501 " pdb=" CBH Y01 R 501 " ideal model delta sinusoidal sigma weight residual -57.13 51.46 -108.59 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" N ARG R 376 " pdb=" C ARG R 376 " pdb=" CA ARG R 376 " pdb=" CB ARG R 376 " ideal model delta harmonic sigma weight residual 122.80 114.15 8.65 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 4146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 941 0.079 - 0.158: 161 0.158 - 0.236: 14 0.236 - 0.315: 3 0.315 - 0.394: 4 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CG LEU B 146 " pdb=" CB LEU B 146 " pdb=" CD1 LEU B 146 " pdb=" CD2 LEU B 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CBG Y01 R 501 " pdb=" CAQ Y01 R 501 " pdb=" CBD Y01 R 501 " pdb=" CBI Y01 R 501 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ARG R 376 " pdb=" N ARG R 376 " pdb=" C ARG R 376 " pdb=" CB ARG R 376 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1120 not shown) Planarity restraints: 1189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 200 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO R 201 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO R 201 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 201 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 174 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO R 175 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 152 " -0.018 2.00e-02 2.50e+03 1.40e-02 4.92e+00 pdb=" CG TRP R 152 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP R 152 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 152 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP R 152 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 152 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 152 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP R 152 " -0.001 2.00e-02 2.50e+03 ... (remaining 1186 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1752 2.80 - 3.33: 6294 3.33 - 3.85: 11771 3.85 - 4.38: 13697 4.38 - 4.90: 23660 Nonbonded interactions: 57174 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.280 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.319 3.040 nonbonded pdb=" O CYS R 114 " pdb=" OG1 THR R 118 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.346 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.354 3.040 ... (remaining 57169 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 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: 2.450 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.880 Find NCS groups from input model: 0.030 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:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 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 0.101 7022 Z= 0.305 Angle : 0.946 14.524 9543 Z= 0.504 Chirality : 0.061 0.394 1123 Planarity : 0.007 0.077 1189 Dihedral : 11.986 108.587 2448 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.12 % 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: -1.45 (0.26), residues: 869 helix: -0.90 (0.23), residues: 383 sheet: 0.10 (0.39), residues: 185 loop : -1.52 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 342 TYR 0.037 0.003 TYR B 59 PHE 0.023 0.003 PHE B 151 TRP 0.038 0.004 TRP R 152 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.28 ( 7020) covalent geometry : angle 0.94574 / 0.50 ( 9541) SS BOND : bond 0.00185 / 0.10 ( 1) SS BOND : angle 0.48947 / 0.27 ( 2) hydrogen bonds : bond 0.23804 / 16.19 ( 381) hydrogen bonds : angle 7.68792 / 5.34 ( 1113) Misc. bond : bond 0.10098 / 5.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7137 (mmp-170) REVERT: B 65 THR cc_start: 0.7138 (m) cc_final: 0.6775 (p) REVERT: B 217 MET cc_start: 0.7681 (ptt) cc_final: 0.6448 (ptt) REVERT: B 269 ILE cc_start: 0.5407 (mm) cc_final: 0.4941 (mt) REVERT: R 105 LYS cc_start: 0.8712 (mttp) cc_final: 0.8510 (mtmt) REVERT: R 126 SER cc_start: 0.8362 (t) cc_final: 0.7868 (p) REVERT: R 145 LYS cc_start: 0.7389 (pttt) cc_final: 0.7160 (pttp) REVERT: R 195 MET cc_start: 0.7015 (mtm) cc_final: 0.6798 (mtt) REVERT: A 25 MET cc_start: 0.6445 (ttm) cc_final: 0.5929 (ttm) REVERT: A 36 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7597 (mtmm) REVERT: A 218 ASN cc_start: 0.7201 (t0) cc_final: 0.6513 (m-40) REVERT: A 253 TYR cc_start: 0.7023 (m-80) cc_final: 0.6536 (m-80) REVERT: A 343 LYS cc_start: 0.6797 (tmtt) cc_final: 0.6445 (tptp) REVERT: A 347 ASP cc_start: 0.4691 (p0) cc_final: 0.4244 (p0) REVERT: A 380 LYS cc_start: 0.7234 (tmtt) cc_final: 0.6852 (tttm) outliers start: 0 outliers final: 1 residues processed: 186 average time/residue: 0.4002 time to fit residues: 78.8077 Evaluate side-chains 104 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN R 191 GLN ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 366 ASN A 236 GLN A 357 HIS ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.149211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.121997 restraints weight = 14769.524| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.84 r_work: 0.3971 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 7022 Z= 0.318 Angle : 0.823 10.980 9543 Z= 0.431 Chirality : 0.051 0.167 1123 Planarity : 0.006 0.066 1189 Dihedral : 7.579 118.152 967 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.89 % Allowed : 13.75 % Favored : 82.36 % 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: -0.48 (0.28), residues: 869 helix: 0.59 (0.26), residues: 381 sheet: -0.25 (0.38), residues: 176 loop : -1.41 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 251 TYR 0.015 0.003 TYR R 237 PHE 0.030 0.003 PHE A 246 TRP 0.015 0.003 TRP B 297 HIS 0.014 0.003 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.32 ( 7020) covalent geometry : angle 0.82213 / 0.43 ( 9541) SS BOND : bond 0.00170 / 0.09 ( 1) SS BOND : angle 2.05897 / 1.18 ( 2) hydrogen bonds : bond 0.06230 / 4.23 ( 381) hydrogen bonds : angle 5.46722 / 3.85 ( 1113) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8589 (ptt) cc_final: 0.8228 (ptt) REVERT: B 234 PHE cc_start: 0.5695 (OUTLIER) cc_final: 0.4324 (t80) REVERT: R 72 MET cc_start: 0.7852 (ttp) cc_final: 0.7543 (ptp) REVERT: R 92 LEU cc_start: 0.7614 (mt) cc_final: 0.7214 (mp) REVERT: R 105 LYS cc_start: 0.8813 (mttp) cc_final: 0.8454 (mtmt) REVERT: R 187 LYS cc_start: 0.5915 (mttt) cc_final: 0.5687 (mptt) REVERT: A 218 ASN cc_start: 0.7291 (t0) cc_final: 0.6512 (m-40) REVERT: A 380 LYS cc_start: 0.7348 (tmtt) cc_final: 0.6815 (tptt) outliers start: 28 outliers final: 13 residues processed: 132 average time/residue: 0.4315 time to fit residues: 60.3254 Evaluate side-chains 106 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.0370 chunk 82 optimal weight: 0.0060 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.5074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN B 293 ASN ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.154539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.128762 restraints weight = 14396.830| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.79 r_work: 0.4084 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7022 Z= 0.137 Angle : 0.667 12.407 9543 Z= 0.337 Chirality : 0.044 0.159 1123 Planarity : 0.004 0.049 1189 Dihedral : 6.678 115.885 965 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.06 % Allowed : 17.08 % Favored : 79.86 % 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: 0.27 (0.29), residues: 869 helix: 1.42 (0.27), residues: 381 sheet: -0.18 (0.38), residues: 189 loop : -1.13 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.022 0.002 TYR A 360 PHE 0.018 0.001 PHE A 219 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 7020) covalent geometry : angle 0.66658 / 0.34 ( 9541) SS BOND : bond 0.01354 / 0.71 ( 1) SS BOND : angle 1.56556 / 0.86 ( 2) hydrogen bonds : bond 0.04539 / 3.10 ( 381) hydrogen bonds : angle 4.78485 / 3.34 ( 1113) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: G 37 LEU cc_start: 0.7113 (mm) cc_final: 0.6859 (mm) REVERT: R 126 SER cc_start: 0.8260 (t) cc_final: 0.7972 (p) REVERT: R 368 ILE cc_start: 0.8582 (pp) cc_final: 0.8347 (pp) REVERT: R 373 MET cc_start: 0.7782 (mtp) cc_final: 0.7504 (tmt) REVERT: R 374 ASN cc_start: 0.7309 (m-40) cc_final: 0.7068 (m-40) REVERT: A 253 TYR cc_start: 0.7188 (m-80) cc_final: 0.6880 (m-10) REVERT: A 380 LYS cc_start: 0.7335 (tmtt) cc_final: 0.6943 (ttpt) outliers start: 22 outliers final: 12 residues processed: 121 average time/residue: 0.4141 time to fit residues: 53.1736 Evaluate side-chains 103 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 71 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.154151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.128267 restraints weight = 14640.648| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.86 r_work: 0.4078 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7022 Z= 0.132 Angle : 0.646 10.769 9543 Z= 0.326 Chirality : 0.043 0.165 1123 Planarity : 0.004 0.060 1189 Dihedral : 6.503 116.427 965 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.89 % Allowed : 17.22 % Favored : 78.89 % 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: 0.50 (0.29), residues: 869 helix: 1.69 (0.27), residues: 385 sheet: -0.25 (0.37), residues: 190 loop : -1.06 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.016 0.002 TYR A 360 PHE 0.014 0.001 PHE A 219 TRP 0.017 0.002 TRP R 326 HIS 0.011 0.001 HIS R 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7020) covalent geometry : angle 0.64531 / 0.33 ( 9541) SS BOND : bond 0.00477 / 0.25 ( 1) SS BOND : angle 1.78316 / 0.98 ( 2) hydrogen bonds : bond 0.04280 / 2.91 ( 381) hydrogen bonds : angle 4.62743 / 3.24 ( 1113) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: B 234 PHE cc_start: 0.5441 (OUTLIER) cc_final: 0.5183 (t80) REVERT: B 293 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.7075 (t0) REVERT: G 37 LEU cc_start: 0.7049 (mm) cc_final: 0.6818 (mm) REVERT: R 126 SER cc_start: 0.8320 (t) cc_final: 0.8023 (p) REVERT: R 368 ILE cc_start: 0.8471 (pp) cc_final: 0.8242 (pp) REVERT: A 253 TYR cc_start: 0.7140 (m-80) cc_final: 0.6797 (m-80) REVERT: A 380 LYS cc_start: 0.7366 (tmtt) cc_final: 0.6960 (ttpt) REVERT: A 390 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8162 (tm-30) outliers start: 28 outliers final: 15 residues processed: 110 average time/residue: 0.4252 time to fit residues: 49.7059 Evaluate side-chains 100 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 98 ASN ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.154353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.128404 restraints weight = 14729.786| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.87 r_work: 0.4079 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7022 Z= 0.129 Angle : 0.654 9.603 9543 Z= 0.326 Chirality : 0.043 0.153 1123 Planarity : 0.004 0.057 1189 Dihedral : 6.421 116.679 965 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.03 % Allowed : 18.33 % Favored : 77.64 % 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: 0.56 (0.29), residues: 869 helix: 1.74 (0.27), residues: 389 sheet: -0.35 (0.37), residues: 192 loop : -0.95 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 336 TYR 0.049 0.002 TYR R 176 PHE 0.011 0.001 PHE B 151 TRP 0.020 0.002 TRP R 326 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7020) covalent geometry : angle 0.65295 / 0.33 ( 9541) SS BOND : bond 0.00510 / 0.27 ( 1) SS BOND : angle 2.11839 / 1.15 ( 2) hydrogen bonds : bond 0.04083 / 2.79 ( 381) hydrogen bonds : angle 4.57441 / 3.22 ( 1113) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5529 (OUTLIER) cc_final: 0.5085 (t80) REVERT: R 92 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7131 (mp) REVERT: R 126 SER cc_start: 0.8311 (t) cc_final: 0.8010 (p) REVERT: R 306 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4608 (pp-130) REVERT: R 373 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5817 (tmt) REVERT: A 253 TYR cc_start: 0.7172 (m-80) cc_final: 0.6817 (m-80) REVERT: A 380 LYS cc_start: 0.7337 (tmtt) cc_final: 0.6758 (tptt) REVERT: A 390 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8128 (tm-30) outliers start: 29 outliers final: 14 residues processed: 110 average time/residue: 0.3932 time to fit residues: 46.1002 Evaluate side-chains 105 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.151971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.125758 restraints weight = 14704.528| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.84 r_work: 0.4046 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7022 Z= 0.160 Angle : 0.676 9.008 9543 Z= 0.341 Chirality : 0.044 0.153 1123 Planarity : 0.004 0.058 1189 Dihedral : 6.514 116.949 965 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.72 % Allowed : 18.06 % Favored : 77.22 % 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: 0.60 (0.29), residues: 869 helix: 1.84 (0.27), residues: 386 sheet: -0.41 (0.37), residues: 194 loop : -0.94 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 310 TYR 0.019 0.002 TYR A 360 PHE 0.014 0.001 PHE B 151 TRP 0.023 0.002 TRP R 326 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 7020) covalent geometry : angle 0.67604 / 0.34 ( 9541) SS BOND : bond 0.00253 / 0.13 ( 1) SS BOND : angle 1.81257 / 0.99 ( 2) hydrogen bonds : bond 0.04211 / 2.87 ( 381) hydrogen bonds : angle 4.68599 / 3.31 ( 1113) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.5036 (t80) REVERT: R 92 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7135 (mp) REVERT: R 126 SER cc_start: 0.8318 (t) cc_final: 0.7914 (p) REVERT: R 235 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7210 (mp0) REVERT: R 306 MET cc_start: 0.5108 (OUTLIER) cc_final: 0.4617 (pp-130) REVERT: A 253 TYR cc_start: 0.7176 (m-80) cc_final: 0.6832 (m-10) REVERT: A 380 LYS cc_start: 0.7375 (tmtt) cc_final: 0.6790 (tptt) REVERT: A 390 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8153 (tm-30) outliers start: 34 outliers final: 18 residues processed: 115 average time/residue: 0.3565 time to fit residues: 43.6418 Evaluate side-chains 112 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 299 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.0270 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.153756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.127716 restraints weight = 14558.858| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.85 r_work: 0.4075 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7022 Z= 0.135 Angle : 0.674 9.351 9543 Z= 0.341 Chirality : 0.044 0.159 1123 Planarity : 0.004 0.055 1189 Dihedral : 6.405 116.359 965 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.03 % Allowed : 19.72 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.29), residues: 869 helix: 1.85 (0.27), residues: 385 sheet: -0.37 (0.37), residues: 193 loop : -0.92 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 310 TYR 0.039 0.002 TYR R 176 PHE 0.018 0.001 PHE R 130 TRP 0.027 0.002 TRP R 326 HIS 0.003 0.001 HIS R 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7020) covalent geometry : angle 0.67339 / 0.34 ( 9541) SS BOND : bond 0.00197 / 0.10 ( 1) SS BOND : angle 2.34063 / 1.28 ( 2) hydrogen bonds : bond 0.04123 / 2.83 ( 381) hydrogen bonds : angle 4.62508 / 3.26 ( 1113) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5636 (OUTLIER) cc_final: 0.5041 (t80) REVERT: R 126 SER cc_start: 0.8285 (t) cc_final: 0.8019 (p) REVERT: R 210 HIS cc_start: 0.6115 (OUTLIER) cc_final: 0.5913 (t-90) REVERT: R 235 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7192 (mp0) REVERT: R 306 MET cc_start: 0.5079 (OUTLIER) cc_final: 0.4666 (pp-130) REVERT: R 329 ILE cc_start: 0.7956 (tp) cc_final: 0.7626 (mp) REVERT: A 253 TYR cc_start: 0.7194 (m-80) cc_final: 0.6883 (m-10) REVERT: A 380 LYS cc_start: 0.7346 (tmtt) cc_final: 0.6792 (tptt) REVERT: A 390 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8080 (tm-30) outliers start: 29 outliers final: 16 residues processed: 115 average time/residue: 0.4454 time to fit residues: 54.2985 Evaluate side-chains 107 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.154609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.128913 restraints weight = 14783.135| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.86 r_work: 0.4092 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7022 Z= 0.127 Angle : 0.687 10.961 9543 Z= 0.343 Chirality : 0.044 0.221 1123 Planarity : 0.004 0.056 1189 Dihedral : 6.324 116.101 965 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.17 % Allowed : 20.42 % Favored : 75.42 % 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: 0.65 (0.29), residues: 869 helix: 1.87 (0.27), residues: 382 sheet: -0.32 (0.37), residues: 197 loop : -0.92 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.028 0.002 TYR R 119 PHE 0.011 0.001 PHE R 130 TRP 0.028 0.002 TRP R 326 HIS 0.003 0.001 HIS R 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 7020) covalent geometry : angle 0.68631 / 0.34 ( 9541) SS BOND : bond 0.00377 / 0.20 ( 1) SS BOND : angle 2.08423 / 1.14 ( 2) hydrogen bonds : bond 0.03953 / 2.70 ( 381) hydrogen bonds : angle 4.55446 / 3.20 ( 1113) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5622 (OUTLIER) cc_final: 0.5089 (t80) REVERT: R 126 SER cc_start: 0.8313 (t) cc_final: 0.7205 (p) REVERT: R 130 PHE cc_start: 0.8498 (m-80) cc_final: 0.7969 (m-80) REVERT: R 155 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6343 (mptp) REVERT: R 235 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7206 (mp0) REVERT: R 306 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.4695 (pp-130) REVERT: R 329 ILE cc_start: 0.7916 (tp) cc_final: 0.7594 (mp) REVERT: R 382 MET cc_start: 0.8745 (ppp) cc_final: 0.8379 (mmt) REVERT: A 253 TYR cc_start: 0.7237 (m-80) cc_final: 0.6935 (m-80) REVERT: A 358 ILE cc_start: 0.8430 (pp) cc_final: 0.8072 (mm) REVERT: A 380 LYS cc_start: 0.7322 (tmtt) cc_final: 0.6772 (tptt) REVERT: A 390 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8128 (tm-30) outliers start: 30 outliers final: 16 residues processed: 109 average time/residue: 0.3784 time to fit residues: 43.9262 Evaluate side-chains 107 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.154765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.129458 restraints weight = 14772.138| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.81 r_work: 0.4101 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7022 Z= 0.129 Angle : 0.720 13.092 9543 Z= 0.354 Chirality : 0.044 0.206 1123 Planarity : 0.004 0.057 1189 Dihedral : 6.300 116.044 965 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.47 % Allowed : 21.94 % Favored : 74.58 % 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: 0.69 (0.29), residues: 869 helix: 1.92 (0.27), residues: 379 sheet: -0.36 (0.37), residues: 202 loop : -0.85 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.027 0.002 TYR R 176 PHE 0.027 0.001 PHE R 93 TRP 0.033 0.002 TRP R 326 HIS 0.005 0.001 HIS R 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 7020) covalent geometry : angle 0.71973 / 0.35 ( 9541) SS BOND : bond 0.00359 / 0.19 ( 1) SS BOND : angle 1.87952 / 1.03 ( 2) hydrogen bonds : bond 0.04006 / 2.71 ( 381) hydrogen bonds : angle 4.57455 / 3.21 ( 1113) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5651 (OUTLIER) cc_final: 0.5014 (t80) REVERT: R 126 SER cc_start: 0.8303 (t) cc_final: 0.7241 (p) REVERT: R 130 PHE cc_start: 0.8494 (m-80) cc_final: 0.7991 (m-80) REVERT: R 155 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6289 (mptp) REVERT: R 187 LYS cc_start: 0.5022 (mtpt) cc_final: 0.4232 (mptm) REVERT: R 306 MET cc_start: 0.5208 (OUTLIER) cc_final: 0.4803 (pp-130) REVERT: R 313 ARG cc_start: 0.7982 (ppt90) cc_final: 0.7415 (ppt90) REVERT: R 329 ILE cc_start: 0.7934 (tp) cc_final: 0.7598 (mp) REVERT: R 382 MET cc_start: 0.8723 (ppp) cc_final: 0.8350 (mmt) REVERT: A 253 TYR cc_start: 0.7226 (m-80) cc_final: 0.6907 (m-80) REVERT: A 380 LYS cc_start: 0.7338 (tmtt) cc_final: 0.6784 (tptt) REVERT: A 390 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8093 (tm-30) outliers start: 25 outliers final: 13 residues processed: 103 average time/residue: 0.4172 time to fit residues: 45.7325 Evaluate side-chains 99 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 69 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.155088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.129859 restraints weight = 14917.799| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.82 r_work: 0.4105 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7022 Z= 0.129 Angle : 0.732 12.453 9543 Z= 0.358 Chirality : 0.044 0.227 1123 Planarity : 0.004 0.056 1189 Dihedral : 6.278 115.920 965 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.92 % Allowed : 23.06 % Favored : 74.03 % 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: 0.64 (0.29), residues: 869 helix: 1.81 (0.27), residues: 385 sheet: -0.25 (0.38), residues: 194 loop : -0.95 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 256 TYR 0.027 0.001 TYR R 176 PHE 0.026 0.001 PHE R 93 TRP 0.032 0.002 TRP R 326 HIS 0.005 0.001 HIS R 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 7020) covalent geometry : angle 0.73144 / 0.36 ( 9541) SS BOND : bond 0.00377 / 0.20 ( 1) SS BOND : angle 1.80576 / 0.99 ( 2) hydrogen bonds : bond 0.03947 / 2.69 ( 381) hydrogen bonds : angle 4.56907 / 3.21 ( 1113) Misc. bond : bond 0.00005 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.5042 (t80) REVERT: R 126 SER cc_start: 0.8335 (t) cc_final: 0.7272 (p) REVERT: R 130 PHE cc_start: 0.8467 (m-80) cc_final: 0.7971 (m-80) REVERT: R 155 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6346 (mptp) REVERT: R 187 LYS cc_start: 0.5051 (mtpt) cc_final: 0.4226 (mptm) REVERT: R 306 MET cc_start: 0.5255 (OUTLIER) cc_final: 0.4856 (pp-130) REVERT: R 314 MET cc_start: 0.6827 (tpp) cc_final: 0.6582 (tpp) REVERT: R 329 ILE cc_start: 0.7937 (tp) cc_final: 0.7617 (mp) REVERT: A 35 GLU cc_start: 0.6739 (pt0) cc_final: 0.6483 (pp20) REVERT: A 253 TYR cc_start: 0.7234 (m-80) cc_final: 0.6935 (m-80) REVERT: A 380 LYS cc_start: 0.7407 (tmtt) cc_final: 0.6855 (tptt) REVERT: A 390 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8114 (tm-30) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 0.3854 time to fit residues: 41.0952 Evaluate side-chains 99 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 237 TYR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.153936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.128680 restraints weight = 14896.242| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.81 r_work: 0.4082 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7022 Z= 0.143 Angle : 0.756 12.523 9543 Z= 0.372 Chirality : 0.045 0.216 1123 Planarity : 0.004 0.055 1189 Dihedral : 6.380 116.051 965 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.36 % Allowed : 23.89 % Favored : 73.75 % 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: 0.55 (0.29), residues: 869 helix: 1.71 (0.27), residues: 387 sheet: -0.28 (0.38), residues: 194 loop : -0.97 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 256 TYR 0.027 0.002 TYR R 176 PHE 0.026 0.001 PHE R 93 TRP 0.030 0.002 TRP R 326 HIS 0.004 0.001 HIS R 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7020) covalent geometry : angle 0.75537 / 0.37 ( 9541) SS BOND : bond 0.00348 / 0.18 ( 1) SS BOND : angle 1.74524 / 0.95 ( 2) hydrogen bonds : bond 0.04087 / 2.77 ( 381) hydrogen bonds : angle 4.65737 / 3.29 ( 1113) Misc. bond : bond 0.00006 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2898.59 seconds wall clock time: 50 minutes 5.40 seconds (3005.40 seconds total)