Starting phenix.real_space_refine on Fri Jul 25 05:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k25_61990/07_2025/9k25_61990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k25_61990/07_2025/9k25_61990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k25_61990/07_2025/9k25_61990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k25_61990/07_2025/9k25_61990.map" model { file = "/net/cci-nas-00/data/ceres_data/9k25_61990/07_2025/9k25_61990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k25_61990/07_2025/9k25_61990.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.076 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 48 5.16 5 C 4568 2.51 5 N 1232 2.21 5 O 1269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7117 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1634 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2258 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 172 Chain: "G" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 227 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2107 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 Chain: "N" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 891 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 4.95, per 1000 atoms: 0.70 Number of scatterers: 7117 At special positions: 0 Unit cell: (75.6, 98.28, 127.44, 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 48 16.00 O 1269 8.00 N 1232 7.00 C 4568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 278 " distance=1.88 Simple disulfide: pdb=" SG CYS I 106 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " 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: 1.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 40.1% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.786A pdb=" N ALA A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 278 removed outlier: 4.093A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.562A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 333 through 352 removed outlier: 4.533A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.953A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.577A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 25 Processing helix chain 'I' and resid 29 through 61 Proline residue: I 37 - end of helix Processing helix chain 'I' and resid 66 through 95 removed outlier: 4.299A pdb=" N SER I 78 " --> pdb=" O HIS I 74 " (cutoff:3.500A) Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 102 through 137 removed outlier: 3.552A pdb=" N ARG I 137 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 removed outlier: 3.516A pdb=" N TRP I 144 " --> pdb=" O ARG I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 165 Processing helix chain 'I' and resid 165 through 172 Processing helix chain 'I' and resid 191 through 207 Processing helix chain 'I' and resid 207 through 227 Processing helix chain 'I' and resid 240 through 270 Proline residue: I 260 - end of helix removed outlier: 3.623A pdb=" N THR I 266 " --> pdb=" O HIS I 262 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER I 270 " --> pdb=" O THR I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 308 removed outlier: 3.637A pdb=" N ALA I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) Proline residue: I 293 - end of helix removed outlier: 4.529A pdb=" N ASN I 298 " --> pdb=" O LEU I 294 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER I 299 " --> pdb=" O ALA I 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS I 300 " --> pdb=" O SER I 296 " (cutoff:3.500A) Proline residue: I 303 - end of helix Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.779A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 7.192A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.501A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.901A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.761A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 180 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.664A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.555A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.591A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 34 through 39 removed outlier: 3.823A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1035 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: 2.17 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2279 1.34 - 1.46: 1868 1.46 - 1.59: 3060 1.59 - 1.71: 0 1.71 - 1.83: 61 Bond restraints: 7268 Sorted by residual: bond pdb=" CA SER I 277 " pdb=" C SER I 277 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.29e-02 6.01e+03 7.38e+00 bond pdb=" CA ARG I 26 " pdb=" C ARG I 26 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.30e-02 5.92e+03 7.02e+00 bond pdb=" N LEU A 12 " pdb=" CA LEU A 12 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.30e+00 bond pdb=" CA LEU I 276 " pdb=" C LEU I 276 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.54e-02 4.22e+03 3.15e+00 bond pdb=" C ARG I 26 " pdb=" N PHE I 27 " ideal model delta sigma weight residual 1.333 1.310 0.024 1.34e-02 5.57e+03 3.11e+00 ... (remaining 7263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 9607 1.53 - 3.07: 261 3.07 - 4.60: 49 4.60 - 6.14: 10 6.14 - 7.67: 1 Bond angle restraints: 9928 Sorted by residual: angle pdb=" N ASP I 19 " pdb=" CA ASP I 19 " pdb=" C ASP I 19 " ideal model delta sigma weight residual 111.07 107.30 3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" N HIS I 184 " pdb=" CA HIS I 184 " pdb=" C HIS I 184 " ideal model delta sigma weight residual 110.10 115.25 -5.15 1.49e+00 4.50e-01 1.20e+01 angle pdb=" N ASN I 282 " pdb=" CA ASN I 282 " pdb=" C ASN I 282 " ideal model delta sigma weight residual 111.28 107.66 3.62 1.09e+00 8.42e-01 1.11e+01 angle pdb=" N ASP I 30 " pdb=" CA ASP I 30 " pdb=" C ASP I 30 " ideal model delta sigma weight residual 111.71 108.47 3.24 1.15e+00 7.56e-01 7.95e+00 angle pdb=" C ILE I 284 " pdb=" CA ILE I 284 " pdb=" CB ILE I 284 " ideal model delta sigma weight residual 112.14 108.38 3.76 1.35e+00 5.49e-01 7.77e+00 ... (remaining 9923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 3672 16.87 - 33.74: 408 33.74 - 50.61: 121 50.61 - 67.48: 17 67.48 - 84.35: 6 Dihedral angle restraints: 4224 sinusoidal: 1374 harmonic: 2850 Sorted by residual: dihedral pdb=" CA ASN A 292 " pdb=" C ASN A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA N 56 " pdb=" C ALA N 56 " pdb=" N SER N 57 " pdb=" CA SER N 57 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 835 0.037 - 0.073: 244 0.073 - 0.110: 83 0.110 - 0.146: 25 0.146 - 0.183: 1 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CG LEU I 276 " pdb=" CB LEU I 276 " pdb=" CD1 LEU I 276 " pdb=" CD2 LEU I 276 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA VAL N 93 " pdb=" N VAL N 93 " pdb=" C VAL N 93 " pdb=" CB VAL N 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1185 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 158 " -0.018 2.00e-02 2.50e+03 1.52e-02 5.74e+00 pdb=" CG TRP I 158 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP I 158 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP I 158 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP I 158 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 158 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 158 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 158 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 158 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP I 158 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR I 23 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C TYR I 23 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR I 23 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG I 24 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 209 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO I 210 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 210 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 210 " -0.025 5.00e-02 4.00e+02 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 829 2.74 - 3.28: 7207 3.28 - 3.82: 11930 3.82 - 4.36: 13522 4.36 - 4.90: 24317 Nonbonded interactions: 57805 Sorted by model distance: nonbonded pdb=" O PRO I 260 " pdb=" OG1 THR I 264 " model vdw 2.206 3.040 nonbonded pdb=" O LYS B 57 " pdb=" OG SER B 74 " model vdw 2.207 3.040 nonbonded pdb=" NH2 ARG A 231 " pdb=" OD2 ASP A 272 " model vdw 2.244 3.120 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLN A 267 " pdb=" ND2 ASN A 271 " model vdw 2.297 3.120 ... (remaining 57800 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: 2.470 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.540 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 7271 Z= 0.209 Angle : 0.638 7.672 9934 Z= 0.362 Chirality : 0.041 0.183 1188 Planarity : 0.004 0.052 1244 Dihedral : 15.933 84.350 2371 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 27.70 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 954 helix: 0.83 (0.27), residues: 369 sheet: -1.71 (0.37), residues: 189 loop : -2.11 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 158 HIS 0.015 0.001 HIS I 74 PHE 0.012 0.001 PHE B 234 TYR 0.015 0.001 TYR I 218 ARG 0.008 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.17128 ( 360) hydrogen bonds : angle 7.12177 ( 1035) SS BOND : bond 0.08684 ( 3) SS BOND : angle 2.41826 ( 6) covalent geometry : bond 0.00360 ( 7268) covalent geometry : angle 0.63568 ( 9928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.784 Fit side-chains REVERT: A 311 TYR cc_start: 0.7208 (m-80) cc_final: 0.6974 (m-80) REVERT: B 219 ARG cc_start: 0.7437 (mtm180) cc_final: 0.7172 (mtt180) REVERT: B 339 TRP cc_start: 0.8518 (m100) cc_final: 0.8280 (m-10) REVERT: I 72 MET cc_start: 0.7474 (mtt) cc_final: 0.7119 (mtt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2126 time to fit residues: 34.5177 Evaluate side-chains 110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.2980 chunk 72 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.189087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153910 restraints weight = 8756.539| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.22 r_work: 0.3818 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7271 Z= 0.122 Angle : 0.555 6.117 9934 Z= 0.293 Chirality : 0.042 0.164 1188 Planarity : 0.004 0.036 1244 Dihedral : 4.290 17.649 1052 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.59 % Allowed : 24.44 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 954 helix: 1.32 (0.27), residues: 374 sheet: -1.40 (0.37), residues: 183 loop : -1.95 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 158 HIS 0.010 0.001 HIS I 74 PHE 0.012 0.001 PHE I 207 TYR 0.012 0.001 TYR I 33 ARG 0.005 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 360) hydrogen bonds : angle 5.19780 ( 1035) SS BOND : bond 0.00339 ( 3) SS BOND : angle 0.53709 ( 6) covalent geometry : bond 0.00265 ( 7268) covalent geometry : angle 0.55532 ( 9928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 392 ASN cc_start: 0.7974 (t0) cc_final: 0.7569 (p0) REVERT: B 90 VAL cc_start: 0.8446 (t) cc_final: 0.8242 (t) REVERT: B 200 VAL cc_start: 0.8669 (m) cc_final: 0.8445 (p) REVERT: B 213 VAL cc_start: 0.8589 (t) cc_final: 0.8343 (m) REVERT: B 234 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: I 33 TYR cc_start: 0.6579 (m-80) cc_final: 0.6366 (m-80) REVERT: N 82 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7892 (tp40) outliers start: 31 outliers final: 16 residues processed: 139 average time/residue: 0.1749 time to fit residues: 33.3951 Evaluate side-chains 131 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 278 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.179702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144747 restraints weight = 8739.347| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.23 r_work: 0.3785 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7271 Z= 0.143 Angle : 0.549 5.393 9934 Z= 0.290 Chirality : 0.043 0.153 1188 Planarity : 0.004 0.038 1244 Dihedral : 4.279 18.295 1052 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.19 % Allowed : 26.52 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 954 helix: 1.51 (0.27), residues: 371 sheet: -1.49 (0.33), residues: 209 loop : -2.01 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 158 HIS 0.004 0.001 HIS I 74 PHE 0.015 0.001 PHE B 199 TYR 0.014 0.001 TYR N 60 ARG 0.005 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 360) hydrogen bonds : angle 4.88308 ( 1035) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.74366 ( 6) covalent geometry : bond 0.00327 ( 7268) covalent geometry : angle 0.54848 ( 9928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.821 Fit side-chains REVERT: A 29 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: A 267 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: A 376 PHE cc_start: 0.8115 (t80) cc_final: 0.7860 (t80) REVERT: A 392 ASN cc_start: 0.8011 (t0) cc_final: 0.7583 (p0) REVERT: B 234 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: I 72 MET cc_start: 0.7896 (mtt) cc_final: 0.7434 (mtt) REVERT: N 67 ARG cc_start: 0.7524 (ptt-90) cc_final: 0.7312 (ptt-90) REVERT: N 82 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7953 (tp40) outliers start: 35 outliers final: 20 residues processed: 149 average time/residue: 0.1717 time to fit residues: 35.3477 Evaluate side-chains 136 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 75 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 0.0060 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.181732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146936 restraints weight = 8746.731| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.22 r_work: 0.3805 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7271 Z= 0.118 Angle : 0.531 6.515 9934 Z= 0.278 Chirality : 0.042 0.199 1188 Planarity : 0.004 0.038 1244 Dihedral : 4.112 18.739 1052 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.19 % Allowed : 27.11 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 954 helix: 1.61 (0.27), residues: 371 sheet: -1.55 (0.33), residues: 211 loop : -2.02 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 339 HIS 0.003 0.001 HIS I 74 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR I 92 ARG 0.005 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 360) hydrogen bonds : angle 4.66036 ( 1035) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.60684 ( 6) covalent geometry : bond 0.00263 ( 7268) covalent geometry : angle 0.53098 ( 9928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.724 Fit side-chains REVERT: A 30 LEU cc_start: 0.9042 (mm) cc_final: 0.8835 (mm) REVERT: A 267 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: A 392 ASN cc_start: 0.7943 (t0) cc_final: 0.7551 (p0) REVERT: G 38 MET cc_start: 0.7590 (mmm) cc_final: 0.7260 (mmm) REVERT: I 72 MET cc_start: 0.7708 (mtt) cc_final: 0.7219 (mtt) REVERT: I 79 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7708 (t0) REVERT: N 67 ARG cc_start: 0.7628 (ptt-90) cc_final: 0.7349 (ptt-90) REVERT: N 82 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7709 (tp40) outliers start: 35 outliers final: 26 residues processed: 142 average time/residue: 0.1650 time to fit residues: 32.3714 Evaluate side-chains 143 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.179136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144200 restraints weight = 8694.048| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.19 r_work: 0.3778 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7271 Z= 0.139 Angle : 0.539 7.241 9934 Z= 0.285 Chirality : 0.042 0.213 1188 Planarity : 0.004 0.039 1244 Dihedral : 4.144 18.787 1052 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 6.52 % Allowed : 25.63 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 954 helix: 1.58 (0.27), residues: 372 sheet: -1.54 (0.32), residues: 209 loop : -1.96 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 199 TYR 0.013 0.001 TYR N 60 ARG 0.004 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 360) hydrogen bonds : angle 4.68371 ( 1035) SS BOND : bond 0.00358 ( 3) SS BOND : angle 0.76456 ( 6) covalent geometry : bond 0.00317 ( 7268) covalent geometry : angle 0.53893 ( 9928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.740 Fit side-chains REVERT: A 267 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 392 ASN cc_start: 0.8086 (t0) cc_final: 0.7556 (p0) REVERT: B 234 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: I 72 MET cc_start: 0.7887 (mtt) cc_final: 0.7511 (mtt) REVERT: I 79 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7889 (t0) REVERT: I 184 HIS cc_start: 0.5672 (OUTLIER) cc_final: 0.5465 (t-90) REVERT: N 82 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7663 (tp40) outliers start: 44 outliers final: 30 residues processed: 154 average time/residue: 0.1657 time to fit residues: 35.1962 Evaluate side-chains 151 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 184 HIS Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.178672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143453 restraints weight = 8727.746| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.20 r_work: 0.3769 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7271 Z= 0.150 Angle : 0.552 7.267 9934 Z= 0.289 Chirality : 0.043 0.235 1188 Planarity : 0.004 0.038 1244 Dihedral : 4.180 19.572 1052 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.07 % Allowed : 25.93 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.27), residues: 954 helix: 1.58 (0.27), residues: 372 sheet: -1.48 (0.34), residues: 192 loop : -1.96 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.001 PHE B 199 TYR 0.013 0.001 TYR N 60 ARG 0.005 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 360) hydrogen bonds : angle 4.68793 ( 1035) SS BOND : bond 0.00265 ( 3) SS BOND : angle 0.77259 ( 6) covalent geometry : bond 0.00346 ( 7268) covalent geometry : angle 0.55178 ( 9928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.759 Fit side-chains REVERT: A 267 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: B 212 ASP cc_start: 0.8602 (t0) cc_final: 0.8359 (t0) REVERT: I 72 MET cc_start: 0.7862 (mtt) cc_final: 0.7487 (mtt) REVERT: I 79 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7910 (t0) REVERT: N 67 ARG cc_start: 0.7551 (ptt-90) cc_final: 0.6948 (ptt-90) REVERT: N 82 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7573 (tp40) outliers start: 41 outliers final: 31 residues processed: 152 average time/residue: 0.1837 time to fit residues: 38.3690 Evaluate side-chains 151 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 84 optimal weight: 0.0470 chunk 54 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.182366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147551 restraints weight = 8652.792| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.20 r_work: 0.3819 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7271 Z= 0.111 Angle : 0.527 7.158 9934 Z= 0.274 Chirality : 0.042 0.248 1188 Planarity : 0.004 0.038 1244 Dihedral : 3.985 18.113 1052 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.33 % Allowed : 27.70 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 954 helix: 1.65 (0.27), residues: 373 sheet: -1.48 (0.32), residues: 209 loop : -1.92 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE I 207 TYR 0.010 0.001 TYR N 60 ARG 0.006 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 360) hydrogen bonds : angle 4.55587 ( 1035) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.58531 ( 6) covalent geometry : bond 0.00245 ( 7268) covalent geometry : angle 0.52710 ( 9928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: B 212 ASP cc_start: 0.8568 (t0) cc_final: 0.8285 (t0) REVERT: I 72 MET cc_start: 0.7842 (mtt) cc_final: 0.7454 (mtt) REVERT: I 79 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7817 (t0) REVERT: N 58 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7372 (mp) REVERT: N 82 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7572 (tp40) outliers start: 36 outliers final: 24 residues processed: 148 average time/residue: 0.2451 time to fit residues: 50.0148 Evaluate side-chains 138 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.173689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137009 restraints weight = 8746.631| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.23 r_work: 0.3687 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7271 Z= 0.175 Angle : 0.583 7.834 9934 Z= 0.304 Chirality : 0.044 0.257 1188 Planarity : 0.004 0.039 1244 Dihedral : 4.267 19.678 1052 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.37 % Allowed : 26.37 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 954 helix: 1.47 (0.27), residues: 378 sheet: -1.58 (0.34), residues: 197 loop : -1.96 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.021 0.001 PHE B 199 TYR 0.015 0.001 TYR N 60 ARG 0.006 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 360) hydrogen bonds : angle 4.71115 ( 1035) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.88645 ( 6) covalent geometry : bond 0.00405 ( 7268) covalent geometry : angle 0.58233 ( 9928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.731 Fit side-chains REVERT: A 267 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: B 126 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7166 (pp) REVERT: B 212 ASP cc_start: 0.8626 (t0) cc_final: 0.8349 (t0) REVERT: B 234 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: I 72 MET cc_start: 0.7868 (mtt) cc_final: 0.7472 (mtt) REVERT: I 79 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7906 (t0) REVERT: N 58 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7386 (mp) REVERT: N 67 ARG cc_start: 0.7459 (ptt-90) cc_final: 0.6915 (ptt-90) REVERT: N 82 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7601 (tp40) outliers start: 43 outliers final: 31 residues processed: 151 average time/residue: 0.2117 time to fit residues: 43.7784 Evaluate side-chains 150 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 40 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139394 restraints weight = 8795.430| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.24 r_work: 0.3715 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7271 Z= 0.141 Angle : 0.558 7.718 9934 Z= 0.290 Chirality : 0.043 0.277 1188 Planarity : 0.004 0.038 1244 Dihedral : 4.171 18.978 1052 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.93 % Allowed : 27.85 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 954 helix: 1.50 (0.27), residues: 378 sheet: -1.57 (0.33), residues: 197 loop : -1.89 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 158 HIS 0.003 0.001 HIS B 225 PHE 0.015 0.001 PHE B 199 TYR 0.013 0.001 TYR N 60 ARG 0.006 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 360) hydrogen bonds : angle 4.65379 ( 1035) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.71700 ( 6) covalent geometry : bond 0.00324 ( 7268) covalent geometry : angle 0.55775 ( 9928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 1.070 Fit side-chains REVERT: A 267 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: A 293 LYS cc_start: 0.8937 (mttt) cc_final: 0.8732 (mttm) REVERT: I 72 MET cc_start: 0.7866 (mtt) cc_final: 0.7464 (mtt) REVERT: I 79 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7882 (t0) REVERT: I 286 MET cc_start: 0.7703 (mmp) cc_final: 0.7418 (mmt) REVERT: N 58 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7386 (mp) REVERT: N 82 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7606 (tp40) outliers start: 40 outliers final: 32 residues processed: 148 average time/residue: 0.2460 time to fit residues: 51.2572 Evaluate side-chains 152 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 0.0010 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.179191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143204 restraints weight = 8816.638| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.25 r_work: 0.3781 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7271 Z= 0.113 Angle : 0.534 7.621 9934 Z= 0.277 Chirality : 0.042 0.275 1188 Planarity : 0.004 0.038 1244 Dihedral : 3.961 17.517 1052 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.33 % Allowed : 28.89 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 954 helix: 1.71 (0.27), residues: 375 sheet: -1.53 (0.32), residues: 214 loop : -1.80 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP I 158 HIS 0.003 0.001 HIS I 74 PHE 0.010 0.001 PHE B 199 TYR 0.010 0.001 TYR N 60 ARG 0.006 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 360) hydrogen bonds : angle 4.55520 ( 1035) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.56007 ( 6) covalent geometry : bond 0.00253 ( 7268) covalent geometry : angle 0.53414 ( 9928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.971 Fit side-chains REVERT: A 267 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: A 293 LYS cc_start: 0.8877 (mttt) cc_final: 0.8612 (mttm) REVERT: I 72 MET cc_start: 0.7690 (mtt) cc_final: 0.7290 (mtt) REVERT: N 58 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7231 (mp) REVERT: N 82 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7509 (tp40) outliers start: 36 outliers final: 27 residues processed: 142 average time/residue: 0.2204 time to fit residues: 43.4889 Evaluate side-chains 141 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 40 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 307 PHE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 89 optimal weight: 0.0570 chunk 86 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.178640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143121 restraints weight = 8742.423| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.22 r_work: 0.3752 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7271 Z= 0.124 Angle : 0.542 8.083 9934 Z= 0.282 Chirality : 0.043 0.269 1188 Planarity : 0.004 0.038 1244 Dihedral : 4.001 17.678 1052 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.04 % Allowed : 29.48 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 954 helix: 1.54 (0.27), residues: 379 sheet: -1.48 (0.32), residues: 221 loop : -1.83 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 158 HIS 0.003 0.001 HIS I 74 PHE 0.015 0.001 PHE A 315 TYR 0.011 0.001 TYR N 60 ARG 0.006 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 360) hydrogen bonds : angle 4.59306 ( 1035) SS BOND : bond 0.00215 ( 3) SS BOND : angle 0.70030 ( 6) covalent geometry : bond 0.00282 ( 7268) covalent geometry : angle 0.54213 ( 9928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4753.66 seconds wall clock time: 86 minutes 31.91 seconds (5191.91 seconds total)