Starting phenix.real_space_refine on Wed Aug 5 00:09:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9okq_70572/08_2026/9okq_70572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9okq_70572/08_2026/9okq_70572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9okq_70572/08_2026/9okq_70572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9okq_70572/08_2026/9okq_70572.map" model { file = "/net/cci-nas-00/data/ceres_data/9okq_70572/08_2026/9okq_70572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9okq_70572/08_2026/9okq_70572.cif" } resolution = 2.9 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= 0.016 sd= 0.090 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 46 5.16 5 C 4966 2.51 5 N 1322 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7662 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1940 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain: "D" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1889 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 13, 'TRANS': 229} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5408 SG CYS D 199 53.439 37.731 80.904 1.00 27.98 S ATOM 5358 SG CYS D 193 48.779 37.366 82.338 1.00 28.01 S ATOM 5414 SG CYS D 200 49.778 36.159 85.854 1.00 27.46 S Restraints were copied for chains: C, E Time building chain proxies: 2.25, per 1000 atoms: 0.29 Number of scatterers: 7662 At special positions: 0 Unit cell: (73.26, 86.58, 110.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 46 16.00 O 1324 8.00 N 1322 7.00 C 4966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 449.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 234 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 197 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 236 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 199 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" ND1 HIS D 230 " pdb="ZN ZN D 402 " - pdb=" NE2 HIS D 232 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 200 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 193 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 234 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 197 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 236 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 199 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" ND1 HIS E 230 " pdb="ZN ZN E 402 " - pdb=" NE2 HIS E 232 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 200 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 193 " Number of angles added : 10 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 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: 50 helices and 6 sheets defined 64.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 1 through 30 Proline residue: B 7 - end of helix removed outlier: 3.593A pdb=" N CYS B 17 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 42 through 53 Processing helix chain 'B' and resid 55 through 77 removed outlier: 4.186A pdb=" N ARG B 77 " --> pdb=" O TRP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 104 removed outlier: 5.370A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 164 through 184 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.533A pdb=" N ILE B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Proline residue: B 199 - end of helix Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 209 through 236 Processing helix chain 'B' and resid 238 through 256 removed outlier: 3.604A pdb=" N VAL B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 30 Proline residue: C 7 - end of helix removed outlier: 3.593A pdb=" N CYS C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 31 through 41 Processing helix chain 'C' and resid 42 through 53 Processing helix chain 'C' and resid 55 through 77 removed outlier: 4.187A pdb=" N ARG C 77 " --> pdb=" O TRP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 104 removed outlier: 5.370A pdb=" N LEU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N SER C 95 " --> pdb=" O HIS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 Processing helix chain 'C' and resid 123 through 144 Processing helix chain 'C' and resid 144 through 154 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 164 through 184 Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.534A pdb=" N ILE C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Proline residue: C 199 - end of helix Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 209 through 236 Processing helix chain 'C' and resid 238 through 256 removed outlier: 3.605A pdb=" N VAL C 244 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.609A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.959A pdb=" N ILE D 114 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 152 through 171 Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 218 through 223 removed outlier: 4.068A pdb=" N GLU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 52 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 100 through 108 removed outlier: 3.609A pdb=" N VAL E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.959A pdb=" N ILE E 114 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 152 through 171 Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 218 through 223 removed outlier: 4.068A pdb=" N GLU E 223 " --> pdb=" O PRO E 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 17 through 27 removed outlier: 6.355A pdb=" N VAL D 19 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER D 13 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER D 21 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER D 11 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL D 23 " --> pdb=" O ASN D 9 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 5 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 10 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU D 58 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 69 through 72 removed outlier: 6.508A pdb=" N GLY D 70 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP D 145 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL D 72 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 190 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS D 200 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 183 through 185 Processing sheet with id=AA4, first strand: chain 'E' and resid 17 through 27 removed outlier: 6.354A pdb=" N VAL E 19 " --> pdb=" O SER E 13 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER E 13 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER E 21 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER E 11 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL E 23 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 5 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL E 10 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU E 58 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.508A pdb=" N GLY E 70 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP E 145 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL E 72 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E 190 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS E 200 " --> pdb=" O CYS E 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 183 through 185 473 hydrogen bonds defined for protein. 1401 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: 1.16 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2482 1.34 - 1.46: 1543 1.46 - 1.58: 3691 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 7796 Sorted by residual: bond pdb=" CB GLU D 212 " pdb=" CG GLU D 212 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 5.90e-01 bond pdb=" CB GLU E 212 " pdb=" CG GLU E 212 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.25e-01 bond pdb=" CG GLU D 212 " pdb=" CD GLU D 212 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.13e-01 bond pdb=" CG GLU E 212 " pdb=" CD GLU E 212 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.01e-01 bond pdb=" CB MET B 151 " pdb=" CG MET B 151 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 4.06e-01 ... (remaining 7791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 10095 0.99 - 1.98: 407 1.98 - 2.97: 68 2.97 - 3.97: 22 3.97 - 4.96: 10 Bond angle restraints: 10602 Sorted by residual: angle pdb=" NE ARG D 63 " pdb=" CZ ARG D 63 " pdb=" NH1 ARG D 63 " ideal model delta sigma weight residual 121.50 119.93 1.57 1.00e+00 1.00e+00 2.47e+00 angle pdb=" C ASN E 195 " pdb=" N HIS E 196 " pdb=" CA HIS E 196 " ideal model delta sigma weight residual 121.54 124.52 -2.98 1.91e+00 2.74e-01 2.44e+00 angle pdb=" C ASN D 195 " pdb=" N HIS D 196 " pdb=" CA HIS D 196 " ideal model delta sigma weight residual 121.54 124.49 -2.95 1.91e+00 2.74e-01 2.38e+00 angle pdb=" NE ARG C 167 " pdb=" CZ ARG C 167 " pdb=" NH1 ARG C 167 " ideal model delta sigma weight residual 121.50 119.98 1.52 1.00e+00 1.00e+00 2.31e+00 angle pdb=" NE ARG B 167 " pdb=" CZ ARG B 167 " pdb=" NH1 ARG B 167 " ideal model delta sigma weight residual 121.50 119.98 1.52 1.00e+00 1.00e+00 2.31e+00 ... (remaining 10597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 4265 14.15 - 28.30: 295 28.30 - 42.45: 88 42.45 - 56.60: 22 56.60 - 70.75: 12 Dihedral angle restraints: 4682 sinusoidal: 1820 harmonic: 2862 Sorted by residual: dihedral pdb=" CA GLU E 212 " pdb=" C GLU E 212 " pdb=" N PHE E 213 " pdb=" CA PHE E 213 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLU D 212 " pdb=" C GLU D 212 " pdb=" N PHE D 213 " pdb=" CA PHE D 213 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA THR E 188 " pdb=" C THR E 188 " pdb=" N ASP E 189 " pdb=" CA ASP E 189 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 811 0.029 - 0.057: 324 0.057 - 0.086: 95 0.086 - 0.114: 78 0.114 - 0.143: 8 Chirality restraints: 1316 Sorted by residual: chirality pdb=" CB ILE D 214 " pdb=" CA ILE D 214 " pdb=" CG1 ILE D 214 " pdb=" CG2 ILE D 214 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CB ILE E 214 " pdb=" CA ILE E 214 " pdb=" CG1 ILE E 214 " pdb=" CG2 ILE E 214 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA VAL B 54 " pdb=" N VAL B 54 " pdb=" C VAL B 54 " pdb=" CB VAL B 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1313 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 240 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO C 241 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 241 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 241 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 240 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 241 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 124 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.018 5.00e-02 4.00e+02 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2341 2.85 - 3.36: 6909 3.36 - 3.87: 12026 3.87 - 4.39: 13014 4.39 - 4.90: 23753 Nonbonded interactions: 58043 Sorted by model distance: nonbonded pdb=" NH1 ARG E 229 " pdb=" O HIS E 230 " model vdw 2.335 3.120 nonbonded pdb=" NH1 ARG D 229 " pdb=" O HIS D 230 " model vdw 2.335 3.120 nonbonded pdb=" O PRO B 238 " pdb=" OG SER B 242 " model vdw 2.400 3.040 nonbonded pdb=" O PRO C 238 " pdb=" OG SER C 242 " model vdw 2.400 3.040 nonbonded pdb=" OG SER E 3 " pdb=" O LEU E 27 " model vdw 2.513 3.040 ... (remaining 58038 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.910 Find NCS groups from input model: 0.060 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.003 0.023 7812 Z= 0.117 Angle : 0.511 7.012 10612 Z= 0.281 Chirality : 0.040 0.143 1316 Planarity : 0.004 0.040 1316 Dihedral : 11.703 70.755 2838 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.60 (0.27), residues: 998 helix: 1.89 (0.22), residues: 586 sheet: 0.95 (0.52), residues: 96 loop : -0.45 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 168 TYR 0.016 0.002 TYR E 160 PHE 0.011 0.001 PHE C 57 TRP 0.007 0.001 TRP C 143 HIS 0.004 0.001 HIS E 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 7796) covalent geometry : angle 0.49862 / 0.28 (10602) hydrogen bonds : bond 0.19219 / 12.85 ( 473) hydrogen bonds : angle 5.62994 / 4.13 ( 1401) metal coordination : bond 0.01016 / 0.54 ( 16) metal coordination : angle 3.64054 / 2.07 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.327 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 227 average time/residue: 0.6818 time to fit residues: 161.4918 Evaluate side-chains 146 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.0060 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 GLN C 144 GLN C 259 GLN D 137 ASN D 239 GLN E 179 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.065097 restraints weight = 15392.591| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.93 r_work: 0.2657 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7812 Z= 0.140 Angle : 0.607 7.961 10612 Z= 0.302 Chirality : 0.041 0.136 1316 Planarity : 0.005 0.049 1316 Dihedral : 4.317 62.631 1074 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.74 % Allowed : 13.37 % Favored : 83.89 % 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: 2.25 (0.27), residues: 998 helix: 2.58 (0.22), residues: 586 sheet: 1.13 (0.54), residues: 96 loop : -0.54 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 77 TYR 0.011 0.001 TYR E 160 PHE 0.018 0.001 PHE C 57 TRP 0.005 0.001 TRP C 143 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 7796) covalent geometry : angle 0.59953 / 0.30 (10602) hydrogen bonds : bond 0.05129 / 3.37 ( 473) hydrogen bonds : angle 4.45411 / 3.25 ( 1401) metal coordination : bond 0.00928 / 0.41 ( 16) metal coordination : angle 3.11675 / 1.78 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 ARG cc_start: 0.7248 (ttm110) cc_final: 0.6979 (ptp90) REVERT: B 108 ARG cc_start: 0.7991 (mmt-90) cc_final: 0.7690 (mmt-90) REVERT: B 110 ASP cc_start: 0.8341 (t0) cc_final: 0.7979 (t0) REVERT: B 118 ASP cc_start: 0.8851 (t0) cc_final: 0.8543 (t0) REVERT: B 193 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8574 (p) REVERT: C 77 ARG cc_start: 0.7291 (ttm110) cc_final: 0.6967 (ptp90) REVERT: C 108 ARG cc_start: 0.8529 (tpp80) cc_final: 0.7664 (mmt-90) REVERT: D 26 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7495 (tm-30) REVERT: D 106 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8917 (mtmm) REVERT: D 180 ASP cc_start: 0.8431 (t0) cc_final: 0.8203 (t0) REVERT: D 190 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8352 (mm-30) REVERT: D 223 GLU cc_start: 0.8737 (pt0) cc_final: 0.8201 (mp0) REVERT: E 28 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8837 (mmtp) REVERT: E 66 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8635 (mmmm) REVERT: E 137 ASN cc_start: 0.8420 (t0) cc_final: 0.8062 (t0) REVERT: E 176 MET cc_start: 0.9111 (mtm) cc_final: 0.8846 (mtm) outliers start: 23 outliers final: 6 residues processed: 163 average time/residue: 0.6562 time to fit residues: 111.9315 Evaluate side-chains 141 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 58 optimal weight: 0.0070 chunk 53 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.0770 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 ASN C 106 ASN C 259 GLN D 137 ASN D 149 GLN D 239 GLN E 137 ASN E 179 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.081346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.062998 restraints weight = 15145.678| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.02 r_work: 0.2653 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7812 Z= 0.117 Angle : 0.542 9.064 10612 Z= 0.267 Chirality : 0.039 0.139 1316 Planarity : 0.005 0.045 1316 Dihedral : 3.681 15.574 1072 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.74 % Allowed : 13.48 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.28), residues: 998 helix: 2.76 (0.22), residues: 590 sheet: 0.99 (0.54), residues: 96 loop : -0.49 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 208 TYR 0.006 0.001 TYR C 58 PHE 0.019 0.001 PHE B 57 TRP 0.003 0.001 TRP C 143 HIS 0.003 0.001 HIS D 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 7796) covalent geometry : angle 0.53439 / 0.27 (10602) hydrogen bonds : bond 0.04138 / 2.71 ( 473) hydrogen bonds : angle 4.15676 / 3.01 ( 1401) metal coordination : bond 0.00808 / 0.36 ( 16) metal coordination : angle 2.95538 / 1.67 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8423 (t0) cc_final: 0.7971 (t0) REVERT: B 118 ASP cc_start: 0.8947 (t0) cc_final: 0.8635 (t0) REVERT: C 108 ARG cc_start: 0.8574 (tpp80) cc_final: 0.7638 (mmt-90) REVERT: C 164 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8137 (mmpt) REVERT: C 185 LYS cc_start: 0.9021 (tppp) cc_final: 0.8790 (ttpt) REVERT: D 26 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 28 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8435 (mmpt) REVERT: D 106 LYS cc_start: 0.9141 (mtmm) cc_final: 0.8882 (mtmm) REVERT: D 109 GLN cc_start: 0.8947 (mp10) cc_final: 0.8616 (mp10) REVERT: D 137 ASN cc_start: 0.8714 (t0) cc_final: 0.8492 (t160) REVERT: D 145 ASP cc_start: 0.8231 (t70) cc_final: 0.7905 (t70) REVERT: D 176 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8824 (mtp) REVERT: D 180 ASP cc_start: 0.8564 (t0) cc_final: 0.8109 (OUTLIER) REVERT: D 190 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8472 (mm-30) REVERT: D 223 GLU cc_start: 0.8732 (pt0) cc_final: 0.8345 (pm20) REVERT: E 28 LYS cc_start: 0.9020 (mtpp) cc_final: 0.8752 (mmtp) REVERT: E 137 ASN cc_start: 0.8612 (t0) cc_final: 0.8219 (t0) REVERT: E 180 ASP cc_start: 0.8500 (t70) cc_final: 0.7996 (t0) outliers start: 23 outliers final: 5 residues processed: 162 average time/residue: 0.6496 time to fit residues: 109.8763 Evaluate side-chains 138 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 177 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 GLN D 149 GLN E 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.078055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.059788 restraints weight = 15958.592| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.99 r_work: 0.2563 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 7812 Z= 0.212 Angle : 0.654 11.182 10612 Z= 0.317 Chirality : 0.042 0.148 1316 Planarity : 0.005 0.081 1316 Dihedral : 3.773 17.521 1072 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.22 % Allowed : 14.08 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.27), residues: 998 helix: 2.77 (0.22), residues: 584 sheet: 0.93 (0.54), residues: 96 loop : -0.55 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 208 TYR 0.008 0.001 TYR E 160 PHE 0.020 0.002 PHE B 57 TRP 0.008 0.001 TRP B 28 HIS 0.005 0.001 HIS E 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.21 ( 7796) covalent geometry : angle 0.63720 / 0.32 (10602) hydrogen bonds : bond 0.05254 / 3.46 ( 473) hydrogen bonds : angle 4.36385 / 3.16 ( 1401) metal coordination : bond 0.01123 / 0.42 ( 16) metal coordination : angle 4.80282 / 2.76 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.8211 (mmt-90) cc_final: 0.7843 (mmt-90) REVERT: B 110 ASP cc_start: 0.8645 (t0) cc_final: 0.8111 (t0) REVERT: B 118 ASP cc_start: 0.8988 (t0) cc_final: 0.8724 (t0) REVERT: C 108 ARG cc_start: 0.8629 (tpp80) cc_final: 0.7872 (mmt-90) REVERT: C 110 ASP cc_start: 0.8755 (t0) cc_final: 0.8414 (t0) REVERT: C 167 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8175 (ttm110) REVERT: C 257 LYS cc_start: 0.7614 (mttm) cc_final: 0.7310 (mttm) REVERT: D 8 GLU cc_start: 0.8080 (mp0) cc_final: 0.7812 (mp0) REVERT: D 26 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7373 (tm-30) REVERT: D 31 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9064 (mtpp) REVERT: D 62 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8122 (mmmm) REVERT: D 106 LYS cc_start: 0.9211 (mtmm) cc_final: 0.8950 (mtmm) REVERT: D 109 GLN cc_start: 0.9038 (mp10) cc_final: 0.8624 (mp10) REVERT: D 137 ASN cc_start: 0.8724 (t0) cc_final: 0.8154 (t0) REVERT: D 145 ASP cc_start: 0.8589 (t70) cc_final: 0.8380 (t70) REVERT: D 176 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8990 (mtm) REVERT: D 180 ASP cc_start: 0.8736 (t0) cc_final: 0.8266 (t0) REVERT: D 223 GLU cc_start: 0.8960 (pt0) cc_final: 0.8508 (pm20) REVERT: E 28 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8835 (mmtp) REVERT: E 66 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8782 (mtmm) REVERT: E 137 ASN cc_start: 0.8721 (t0) cc_final: 0.8306 (t0) REVERT: E 180 ASP cc_start: 0.8870 (t70) cc_final: 0.8507 (t0) outliers start: 27 outliers final: 3 residues processed: 152 average time/residue: 0.6908 time to fit residues: 109.4446 Evaluate side-chains 135 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 GLN D 239 GLN E 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.078772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.060827 restraints weight = 15597.532| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.98 r_work: 0.2583 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7812 Z= 0.146 Angle : 0.594 7.731 10612 Z= 0.286 Chirality : 0.040 0.141 1316 Planarity : 0.004 0.047 1316 Dihedral : 3.682 17.017 1072 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.79 % Allowed : 16.71 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.28), residues: 998 helix: 2.95 (0.22), residues: 582 sheet: 0.82 (0.55), residues: 96 loop : -0.60 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 208 TYR 0.009 0.001 TYR C 114 PHE 0.015 0.001 PHE B 57 TRP 0.004 0.001 TRP B 145 HIS 0.003 0.001 HIS E 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7796) covalent geometry : angle 0.58568 / 0.29 (10602) hydrogen bonds : bond 0.04390 / 2.87 ( 473) hydrogen bonds : angle 4.15635 / 2.99 ( 1401) metal coordination : bond 0.00772 / 0.32 ( 16) metal coordination : angle 3.32611 / 1.89 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ARG cc_start: 0.9026 (mpp80) cc_final: 0.8745 (mmm-85) REVERT: B 108 ARG cc_start: 0.8258 (mmt-90) cc_final: 0.7988 (mmt-90) REVERT: B 110 ASP cc_start: 0.8697 (t0) cc_final: 0.8246 (t0) REVERT: B 118 ASP cc_start: 0.9022 (t0) cc_final: 0.8791 (t0) REVERT: C 108 ARG cc_start: 0.8633 (tpp80) cc_final: 0.7730 (mmt-90) REVERT: C 257 LYS cc_start: 0.7603 (mttm) cc_final: 0.7284 (mttm) REVERT: D 26 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 31 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9018 (mtpp) REVERT: D 109 GLN cc_start: 0.9114 (mp10) cc_final: 0.8688 (mp10) REVERT: D 125 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8703 (mt-10) REVERT: D 137 ASN cc_start: 0.8747 (t0) cc_final: 0.8112 (t160) REVERT: D 145 ASP cc_start: 0.8661 (t70) cc_final: 0.8359 (t70) REVERT: D 146 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8146 (tp30) REVERT: D 180 ASP cc_start: 0.8736 (t0) cc_final: 0.8261 (OUTLIER) REVERT: D 212 GLU cc_start: 0.8903 (pm20) cc_final: 0.8681 (pm20) REVERT: D 223 GLU cc_start: 0.8994 (pt0) cc_final: 0.8541 (pm20) REVERT: E 109 GLN cc_start: 0.9333 (mt0) cc_final: 0.9080 (mp10) REVERT: E 137 ASN cc_start: 0.8758 (t0) cc_final: 0.8416 (t0) REVERT: E 156 GLN cc_start: 0.8540 (tt0) cc_final: 0.8265 (mt0) REVERT: E 180 ASP cc_start: 0.8907 (t70) cc_final: 0.8576 (t0) outliers start: 15 outliers final: 4 residues processed: 154 average time/residue: 0.6940 time to fit residues: 111.3502 Evaluate side-chains 132 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 177 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 61 optimal weight: 0.0370 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 0.0470 chunk 45 optimal weight: 0.0170 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 GLN D 239 GLN E 165 GLN E 179 HIS E 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.062404 restraints weight = 14819.415| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.93 r_work: 0.2650 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7812 Z= 0.118 Angle : 0.594 8.106 10612 Z= 0.288 Chirality : 0.039 0.192 1316 Planarity : 0.004 0.046 1316 Dihedral : 3.584 16.253 1072 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.43 % Allowed : 17.78 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.28), residues: 998 helix: 3.04 (0.22), residues: 582 sheet: 0.77 (0.56), residues: 96 loop : -0.60 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 208 TYR 0.011 0.001 TYR C 114 PHE 0.014 0.001 PHE C 57 TRP 0.007 0.001 TRP B 145 HIS 0.002 0.000 HIS D 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7796) covalent geometry : angle 0.59028 / 0.29 (10602) hydrogen bonds : bond 0.03531 / 2.27 ( 473) hydrogen bonds : angle 3.94957 / 2.82 ( 1401) metal coordination : bond 0.00640 / 0.34 ( 16) metal coordination : angle 2.20189 / 1.24 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ARG cc_start: 0.9012 (mpp80) cc_final: 0.8723 (mmm-85) REVERT: B 108 ARG cc_start: 0.8300 (mmt-90) cc_final: 0.7981 (mmt-90) REVERT: B 110 ASP cc_start: 0.8711 (t0) cc_final: 0.8260 (t0) REVERT: B 118 ASP cc_start: 0.8998 (t0) cc_final: 0.8753 (t0) REVERT: C 108 ARG cc_start: 0.8596 (tpp80) cc_final: 0.7669 (mmt-90) REVERT: C 110 ASP cc_start: 0.8753 (t0) cc_final: 0.8452 (t0) REVERT: C 257 LYS cc_start: 0.7548 (mttm) cc_final: 0.7239 (mttm) REVERT: D 8 GLU cc_start: 0.7931 (mp0) cc_final: 0.7654 (mp0) REVERT: D 26 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7260 (tm-30) REVERT: D 66 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8757 (mtmm) REVERT: D 109 GLN cc_start: 0.9123 (mp10) cc_final: 0.8686 (mp10) REVERT: D 125 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8594 (mt-10) REVERT: D 137 ASN cc_start: 0.8788 (t0) cc_final: 0.8157 (t0) REVERT: D 145 ASP cc_start: 0.8571 (t70) cc_final: 0.8319 (t70) REVERT: D 146 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8078 (tp30) REVERT: D 180 ASP cc_start: 0.8603 (t0) cc_final: 0.8103 (t0) REVERT: D 223 GLU cc_start: 0.8996 (pt0) cc_final: 0.8653 (pm20) REVERT: E 137 ASN cc_start: 0.8803 (t0) cc_final: 0.8456 (t0) REVERT: E 180 ASP cc_start: 0.8872 (t70) cc_final: 0.8593 (t0) outliers start: 12 outliers final: 3 residues processed: 145 average time/residue: 0.6530 time to fit residues: 98.8095 Evaluate side-chains 130 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN D 149 GLN D 239 GLN E 179 HIS E 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.063291 restraints weight = 15797.744| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.97 r_work: 0.2631 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7812 Z= 0.118 Angle : 0.584 9.402 10612 Z= 0.282 Chirality : 0.039 0.144 1316 Planarity : 0.004 0.044 1316 Dihedral : 3.562 15.742 1072 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.31 % Allowed : 18.38 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.28), residues: 998 helix: 3.01 (0.22), residues: 586 sheet: 1.06 (0.62), residues: 76 loop : -0.68 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 208 TYR 0.010 0.001 TYR C 58 PHE 0.016 0.001 PHE C 57 TRP 0.005 0.000 TRP B 73 HIS 0.002 0.001 HIS D 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7796) covalent geometry : angle 0.57845 / 0.28 (10602) hydrogen bonds : bond 0.03606 / 2.35 ( 473) hydrogen bonds : angle 3.95346 / 2.83 ( 1401) metal coordination : bond 0.00576 / 0.25 ( 16) metal coordination : angle 2.65581 / 1.50 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8740 (tm) REVERT: B 30 ARG cc_start: 0.8996 (mpp80) cc_final: 0.8704 (mmm-85) REVERT: B 108 ARG cc_start: 0.8345 (mmt-90) cc_final: 0.8030 (mmt-90) REVERT: B 110 ASP cc_start: 0.8736 (t0) cc_final: 0.8282 (t0) REVERT: B 118 ASP cc_start: 0.9000 (t0) cc_final: 0.8735 (t0) REVERT: C 108 ARG cc_start: 0.8593 (tpp80) cc_final: 0.7674 (mmt-90) REVERT: C 110 ASP cc_start: 0.8769 (t0) cc_final: 0.8474 (t0) REVERT: C 257 LYS cc_start: 0.7538 (mttm) cc_final: 0.7222 (mttm) REVERT: D 8 GLU cc_start: 0.7860 (mp0) cc_final: 0.7443 (mp0) REVERT: D 109 GLN cc_start: 0.9150 (mp10) cc_final: 0.8708 (mp10) REVERT: D 125 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8619 (mt-10) REVERT: D 137 ASN cc_start: 0.8704 (t0) cc_final: 0.8029 (t0) REVERT: D 145 ASP cc_start: 0.8570 (t70) cc_final: 0.8302 (t70) REVERT: D 146 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7996 (tp30) REVERT: D 180 ASP cc_start: 0.8627 (t0) cc_final: 0.8098 (t0) REVERT: D 223 GLU cc_start: 0.9051 (pt0) cc_final: 0.8832 (pm20) REVERT: E 28 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8528 (mmmm) REVERT: E 137 ASN cc_start: 0.8844 (t0) cc_final: 0.8461 (t0) REVERT: E 180 ASP cc_start: 0.8959 (t70) cc_final: 0.8685 (t0) outliers start: 11 outliers final: 5 residues processed: 137 average time/residue: 0.6662 time to fit residues: 95.2104 Evaluate side-chains 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN D 149 GLN D 239 GLN E 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.059831 restraints weight = 15692.966| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.05 r_work: 0.2608 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7812 Z= 0.134 Angle : 0.632 10.431 10612 Z= 0.304 Chirality : 0.039 0.139 1316 Planarity : 0.004 0.045 1316 Dihedral : 3.594 20.621 1072 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.43 % Allowed : 19.09 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.28), residues: 998 helix: 3.05 (0.22), residues: 586 sheet: 1.23 (0.66), residues: 66 loop : -0.70 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 208 TYR 0.010 0.001 TYR C 114 PHE 0.021 0.001 PHE B 57 TRP 0.004 0.000 TRP B 73 HIS 0.002 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 7796) covalent geometry : angle 0.62586 / 0.30 (10602) hydrogen bonds : bond 0.03785 / 2.48 ( 473) hydrogen bonds : angle 3.98062 / 2.84 ( 1401) metal coordination : bond 0.00646 / 0.27 ( 16) metal coordination : angle 2.86105 / 1.62 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8717 (tm) REVERT: B 30 ARG cc_start: 0.9038 (mpp80) cc_final: 0.8742 (mmm-85) REVERT: B 108 ARG cc_start: 0.8355 (mmt-90) cc_final: 0.8040 (mmt-90) REVERT: B 110 ASP cc_start: 0.8767 (t0) cc_final: 0.8306 (t0) REVERT: B 173 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8594 (mmm) REVERT: B 259 GLN cc_start: 0.7359 (tt0) cc_final: 0.7075 (tp-100) REVERT: C 108 ARG cc_start: 0.8616 (tpp80) cc_final: 0.7714 (mmt-90) REVERT: C 110 ASP cc_start: 0.8788 (t0) cc_final: 0.8488 (t0) REVERT: C 257 LYS cc_start: 0.7530 (mttm) cc_final: 0.7225 (mttm) REVERT: D 8 GLU cc_start: 0.7909 (mp0) cc_final: 0.7609 (mp0) REVERT: D 28 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8394 (mmmm) REVERT: D 109 GLN cc_start: 0.9146 (mp10) cc_final: 0.8697 (mp10) REVERT: D 125 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8666 (mt-10) REVERT: D 137 ASN cc_start: 0.8800 (t0) cc_final: 0.8139 (t0) REVERT: D 145 ASP cc_start: 0.8616 (t70) cc_final: 0.8355 (t70) REVERT: D 146 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8042 (tp30) REVERT: D 180 ASP cc_start: 0.8677 (t0) cc_final: 0.8145 (OUTLIER) REVERT: D 223 GLU cc_start: 0.9096 (pt0) cc_final: 0.8879 (pm20) REVERT: E 28 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8513 (mmmm) REVERT: E 66 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8851 (mtmm) REVERT: E 137 ASN cc_start: 0.8891 (t0) cc_final: 0.8500 (t0) outliers start: 12 outliers final: 5 residues processed: 144 average time/residue: 0.6479 time to fit residues: 97.2920 Evaluate side-chains 125 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 177 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 149 GLN D 165 GLN D 239 GLN E 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.059497 restraints weight = 15142.692| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.95 r_work: 0.2587 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7812 Z= 0.162 Angle : 0.660 10.642 10612 Z= 0.315 Chirality : 0.040 0.136 1316 Planarity : 0.004 0.044 1316 Dihedral : 3.656 20.854 1072 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.43 % Allowed : 19.09 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.28), residues: 998 helix: 3.02 (0.22), residues: 586 sheet: 0.72 (0.58), residues: 86 loop : -0.56 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 208 TYR 0.010 0.001 TYR C 114 PHE 0.008 0.001 PHE C 34 TRP 0.003 0.001 TRP B 73 HIS 0.002 0.001 HIS E 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 7796) covalent geometry : angle 0.65286 / 0.31 (10602) hydrogen bonds : bond 0.04205 / 2.77 ( 473) hydrogen bonds : angle 4.08670 / 2.93 ( 1401) metal coordination : bond 0.00782 / 0.30 ( 16) metal coordination : angle 3.22405 / 1.82 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.8454 (mmt-90) cc_final: 0.8201 (mmt-90) REVERT: B 110 ASP cc_start: 0.8768 (t0) cc_final: 0.8302 (t0) REVERT: B 258 LYS cc_start: 0.8049 (tptp) cc_final: 0.7823 (tptp) REVERT: B 259 GLN cc_start: 0.7013 (tt0) cc_final: 0.6471 (tp-100) REVERT: C 110 ASP cc_start: 0.8784 (t0) cc_final: 0.8503 (t0) REVERT: C 257 LYS cc_start: 0.7638 (mttm) cc_final: 0.7341 (mttm) REVERT: D 28 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8536 (mmmm) REVERT: D 109 GLN cc_start: 0.9192 (mp10) cc_final: 0.8678 (mp10) REVERT: D 137 ASN cc_start: 0.8792 (t0) cc_final: 0.8123 (t0) REVERT: D 145 ASP cc_start: 0.8699 (t70) cc_final: 0.8448 (t70) REVERT: D 180 ASP cc_start: 0.8737 (t0) cc_final: 0.8272 (t0) REVERT: E 28 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8529 (mmmm) REVERT: E 137 ASN cc_start: 0.8875 (t0) cc_final: 0.8476 (t0) outliers start: 12 outliers final: 6 residues processed: 132 average time/residue: 0.7387 time to fit residues: 101.7449 Evaluate side-chains 125 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 82 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 64 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 149 GLN D 165 GLN D 239 GLN E 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.060966 restraints weight = 14885.796| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.95 r_work: 0.2634 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7812 Z= 0.121 Angle : 0.651 11.074 10612 Z= 0.314 Chirality : 0.039 0.158 1316 Planarity : 0.004 0.047 1316 Dihedral : 3.610 21.064 1072 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.84 % Allowed : 20.05 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.28), residues: 998 helix: 3.08 (0.22), residues: 586 sheet: 1.32 (0.66), residues: 66 loop : -0.70 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 208 TYR 0.012 0.001 TYR C 114 PHE 0.011 0.001 PHE B 57 TRP 0.006 0.001 TRP B 145 HIS 0.002 0.000 HIS D 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7796) covalent geometry : angle 0.64764 / 0.31 (10602) hydrogen bonds : bond 0.03517 / 2.31 ( 473) hydrogen bonds : angle 3.94134 / 2.82 ( 1401) metal coordination : bond 0.00533 / 0.27 ( 16) metal coordination : angle 2.37247 / 1.35 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ARG cc_start: 0.9125 (mpp80) cc_final: 0.8796 (mmm-85) REVERT: B 74 LEU cc_start: 0.8745 (mt) cc_final: 0.8512 (tm) REVERT: B 108 ARG cc_start: 0.8421 (mmt-90) cc_final: 0.8123 (mmt-90) REVERT: B 110 ASP cc_start: 0.8766 (t0) cc_final: 0.8317 (t0) REVERT: B 257 LYS cc_start: 0.7897 (tttt) cc_final: 0.7655 (ttmm) REVERT: C 108 ARG cc_start: 0.8467 (tpp80) cc_final: 0.7593 (mmt-90) REVERT: C 110 ASP cc_start: 0.8780 (t0) cc_final: 0.8494 (t0) REVERT: C 257 LYS cc_start: 0.7413 (mttm) cc_final: 0.7145 (mttm) REVERT: D 28 LYS cc_start: 0.8721 (mmmm) cc_final: 0.8310 (mmmm) REVERT: D 109 GLN cc_start: 0.9181 (mp10) cc_final: 0.8675 (mp10) REVERT: D 137 ASN cc_start: 0.8789 (t0) cc_final: 0.8188 (t0) REVERT: D 145 ASP cc_start: 0.8649 (t70) cc_final: 0.8398 (t70) REVERT: D 180 ASP cc_start: 0.8743 (t0) cc_final: 0.8277 (OUTLIER) REVERT: E 28 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8479 (mmmm) REVERT: E 137 ASN cc_start: 0.8890 (t0) cc_final: 0.8503 (t0) outliers start: 7 outliers final: 4 residues processed: 134 average time/residue: 0.7019 time to fit residues: 98.0666 Evaluate side-chains 123 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain D residue 177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 149 GLN D 165 GLN D 239 GLN E 179 HIS E 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.060429 restraints weight = 15060.030| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.94 r_work: 0.2602 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7812 Z= 0.154 Angle : 0.680 10.366 10612 Z= 0.322 Chirality : 0.040 0.147 1316 Planarity : 0.004 0.044 1316 Dihedral : 3.640 21.020 1072 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.95 % Allowed : 20.29 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.28), residues: 998 helix: 3.05 (0.22), residues: 584 sheet: 0.73 (0.58), residues: 86 loop : -0.61 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 208 TYR 0.011 0.001 TYR C 114 PHE 0.009 0.001 PHE C 34 TRP 0.007 0.001 TRP B 73 HIS 0.002 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.15 ( 7796) covalent geometry : angle 0.67411 / 0.32 (10602) hydrogen bonds : bond 0.03992 / 2.63 ( 473) hydrogen bonds : angle 4.07707 / 2.92 ( 1401) metal coordination : bond 0.00689 / 0.26 ( 16) metal coordination : angle 3.09198 / 1.75 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.24 seconds wall clock time: 40 minutes 53.33 seconds (2453.33 seconds total)