Starting phenix.real_space_refine on Wed Aug 5 00:18:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9okp_70571/08_2026/9okp_70571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9okp_70571/08_2026/9okp_70571.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 { model { file = "/net/cci-nas-00/data/ceres_data/9okp_70571/08_2026/9okp_70571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9okp_70571/08_2026/9okp_70571.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9okp_70571/08_2026/9okp_70571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9okp_70571/08_2026/9okp_70571.map" } 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= 0.017 sd= 0.099 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 4966 2.51 5 N 1329 2.21 5 O 1343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 7696 Number of models: 1 Model: "" Number of chains: 6 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: "C" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1926 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 10, 'TRANS': 247} Chain: "D" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain: "E" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5394 SG CYS D 199 51.778 35.260 81.640 1.00 34.89 S ATOM 5344 SG CYS D 193 47.034 34.658 82.995 1.00 34.11 S ATOM 5400 SG CYS D 200 48.367 33.395 86.506 1.00 34.02 S ATOM 7275 SG CYS E 199 17.863 45.083 81.671 1.00 36.00 S ATOM 7225 SG CYS E 193 22.607 45.691 83.021 1.00 35.60 S ATOM 7281 SG CYS E 200 21.277 46.957 86.531 1.00 35.19 S Time building chain proxies: 1.76, per 1000 atoms: 0.23 Number of scatterers: 7696 At special positions: 0 Unit cell: (70.596, 82.584, 111.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 6 15.00 Mg 2 11.99 O 1343 8.00 N 1329 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: 0.42 Conformation dependent library (CDL) restraints added in 295.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 236 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 234 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 197 " pdb="ZN ZN D 303 " - pdb=" SG CYS D 199 " pdb=" ZN D 304 " pdb="ZN ZN D 304 " - pdb=" NE2 HIS D 232 " pdb="ZN ZN D 304 " - pdb=" ND1 HIS D 230 " pdb="ZN ZN D 304 " - pdb=" SG CYS D 200 " pdb="ZN ZN D 304 " - pdb=" SG CYS D 193 " pdb=" ZN E 303 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 236 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 234 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 197 " pdb="ZN ZN E 303 " - pdb=" SG CYS E 199 " pdb=" ZN E 304 " pdb="ZN ZN E 304 " - pdb=" NE2 HIS E 232 " pdb="ZN ZN E 304 " - pdb=" ND1 HIS E 230 " pdb="ZN ZN E 304 " - pdb=" SG CYS E 200 " pdb="ZN ZN E 304 " - pdb=" SG CYS E 193 " Number of angles added : 8 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 64.7% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 1 through 30 Proline residue: B 7 - end of helix removed outlier: 3.694A pdb=" N CYS B 17 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 3.844A 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 41 through 53 removed outlier: 3.916A pdb=" N GLY B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 77 Processing helix chain 'B' and resid 81 through 104 removed outlier: 5.062A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.088A 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 removed outlier: 3.709A pdb=" N LEU B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) 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 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: 3.518A pdb=" N MET B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 30 Proline residue: C 7 - end of helix removed outlier: 3.622A pdb=" N CYS C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 3.792A 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 41 through 53 removed outlier: 3.980A pdb=" N GLY C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 77 Processing helix chain 'C' and resid 81 through 104 removed outlier: 4.904A pdb=" N LEU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 4.987A 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 removed outlier: 3.658A pdb=" N LEU C 127 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) 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 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 255 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 Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.867A 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 136 removed outlier: 3.550A pdb=" N LEU D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 171 Processing helix chain 'D' and resid 212 through 224 Proline residue: D 219 - end of helix removed outlier: 3.581A 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 Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.868A 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 136 removed outlier: 3.550A pdb=" N LEU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 171 Processing helix chain 'E' and resid 212 through 224 Proline residue: E 219 - end of helix removed outlier: 3.581A 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: 6.498A pdb=" N VAL D 19 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER D 13 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER D 21 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER D 11 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL D 23 " --> pdb=" O ASN D 9 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 5 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 10 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 6.420A 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: 6.724A pdb=" N LEU D 142 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL D 177 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU D 144 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU D 33 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 32 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU D 192 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR D 34 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU D 194 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU D 36 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.078A 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 'D' and resid 235 through 236 removed outlier: 4.156A pdb=" N ARG D 235 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 17 through 27 removed outlier: 6.497A pdb=" N VAL E 19 " --> pdb=" O SER E 13 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER E 13 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER E 21 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER E 11 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL E 23 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL E 5 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL E 10 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU E 58 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.724A pdb=" N LEU E 142 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL E 177 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU E 144 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU E 33 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE E 32 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU E 192 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR E 34 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU E 194 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU E 36 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS E 200 " --> pdb=" O CYS E 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 185 Processing sheet with id=AA8, first strand: chain 'E' and resid 235 through 236 removed outlier: 4.156A pdb=" N ARG E 235 " --> pdb=" O VAL E 243 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1365 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: 0.87 Time building geometry restraints manager: 0.60 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: 2476 1.34 - 1.46: 1452 1.46 - 1.58: 3814 1.58 - 1.69: 10 1.69 - 1.81: 80 Bond restraints: 7832 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.38e+01 bond pdb=" C4 ATP D 301 " pdb=" C5 ATP D 301 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.36e+01 bond pdb=" C5 ATP D 301 " pdb=" C6 ATP D 301 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C8 ATP D 301 " pdb=" N7 ATP D 301 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.17e+01 ... (remaining 7827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 10628 4.26 - 8.52: 31 8.52 - 12.78: 2 12.78 - 17.04: 2 17.04 - 21.30: 2 Bond angle restraints: 10665 Sorted by residual: angle pdb=" PB ATP D 301 " pdb=" O3B ATP D 301 " pdb=" PG ATP D 301 " ideal model delta sigma weight residual 139.87 118.57 21.30 1.00e+00 1.00e+00 4.54e+02 angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 118.58 21.29 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 123.07 13.76 1.00e+00 1.00e+00 1.89e+02 angle pdb=" PA ATP D 301 " pdb=" O3A ATP D 301 " pdb=" PB ATP D 301 " ideal model delta sigma weight residual 136.83 123.10 13.73 1.00e+00 1.00e+00 1.88e+02 angle pdb=" C5 ATP D 301 " pdb=" C4 ATP D 301 " pdb=" N3 ATP D 301 " ideal model delta sigma weight residual 126.80 118.82 7.98 1.00e+00 1.00e+00 6.36e+01 ... (remaining 10660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4368 16.73 - 33.47: 286 33.47 - 50.20: 51 50.20 - 66.93: 20 66.93 - 83.67: 6 Dihedral angle restraints: 4731 sinusoidal: 1881 harmonic: 2850 Sorted by residual: dihedral pdb=" CA ARG D 138 " pdb=" C ARG D 138 " pdb=" N PRO D 139 " pdb=" CA PRO D 139 " ideal model delta harmonic sigma weight residual 180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ARG E 138 " pdb=" C ARG E 138 " pdb=" N PRO E 139 " pdb=" CA PRO E 139 " ideal model delta harmonic sigma weight residual 180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB LYS B 258 " pdb=" CG LYS B 258 " pdb=" CD LYS B 258 " pdb=" CE LYS B 258 " ideal model delta sinusoidal sigma weight residual -180.00 -123.66 -56.34 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 4728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 636 0.024 - 0.048: 391 0.048 - 0.073: 184 0.073 - 0.097: 67 0.097 - 0.121: 40 Chirality restraints: 1318 Sorted by residual: chirality pdb=" CA PRO E 219 " pdb=" N PRO E 219 " pdb=" C PRO E 219 " pdb=" CB PRO E 219 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE E 61 " pdb=" N ILE E 61 " pdb=" C ILE E 61 " pdb=" CB ILE E 61 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA ILE D 61 " pdb=" N ILE D 61 " pdb=" C ILE D 61 " pdb=" CB ILE D 61 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 1315 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 240 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 241 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 240 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 241 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 241 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 241 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 55 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO C 56 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " -0.018 5.00e-02 4.00e+02 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 14 2.46 - 3.07: 4939 3.07 - 3.68: 10708 3.68 - 4.29: 16080 4.29 - 4.90: 27480 Nonbonded interactions: 59221 Sorted by model distance: nonbonded pdb=" O3G ATP E 301 " pdb="MG MG E 302 " model vdw 1.851 2.170 nonbonded pdb=" O3G ATP D 301 " pdb="MG MG D 302 " model vdw 1.852 2.170 nonbonded pdb=" OG SER D 44 " pdb="MG MG D 302 " model vdw 2.074 2.170 nonbonded pdb=" OG SER E 44 " pdb="MG MG E 302 " model vdw 2.075 2.170 nonbonded pdb=" OE1 GLN E 74 " pdb="MG MG E 302 " model vdw 2.118 2.170 ... (remaining 59216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 258) 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: 0.150 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: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.140 Find NCS groups from input model: 0.120 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:5.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.005 0.080 7848 Z= 0.285 Angle : 0.745 21.299 10673 Z= 0.520 Chirality : 0.041 0.121 1318 Planarity : 0.004 0.035 1313 Dihedral : 12.411 83.667 2895 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.27), residues: 994 helix: 2.35 (0.22), residues: 580 sheet: 1.33 (0.59), residues: 86 loop : -0.41 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 204 TYR 0.018 0.002 TYR D 160 PHE 0.012 0.002 PHE B 57 TRP 0.012 0.001 TRP C 143 HIS 0.005 0.001 HIS D 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.28 ( 7832) covalent geometry : angle 0.74440 / 0.52 (10665) hydrogen bonds : bond 0.13998 / 8.93 ( 461) hydrogen bonds : angle 5.56908 / 3.95 ( 1365) metal coordination : bond 0.00870 / 0.48 ( 16) metal coordination : angle 1.27252 / 0.69 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 ASP cc_start: 0.7319 (m-30) cc_final: 0.7038 (m-30) outliers start: 0 outliers final: 1 residues processed: 212 average time/residue: 0.6436 time to fit residues: 142.4242 Evaluate side-chains 140 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 GLN D 137 ASN D 224 GLN E 115 ASN E 137 ASN E 224 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.062158 restraints weight = 15407.797| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.05 r_work: 0.2673 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7848 Z= 0.150 Angle : 0.634 7.329 10673 Z= 0.318 Chirality : 0.040 0.144 1318 Planarity : 0.005 0.040 1313 Dihedral : 6.561 63.034 1138 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.56 % Allowed : 13.29 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.28), residues: 994 helix: 2.45 (0.22), residues: 599 sheet: 1.24 (0.55), residues: 96 loop : -0.81 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 17 TYR 0.009 0.001 TYR D 77 PHE 0.013 0.001 PHE B 57 TRP 0.007 0.001 TRP B 73 HIS 0.003 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 7832) covalent geometry : angle 0.63359 / 0.32 (10665) hydrogen bonds : bond 0.04735 / 3.19 ( 461) hydrogen bonds : angle 4.39423 / 3.19 ( 1365) metal coordination : bond 0.00524 / 0.21 ( 16) metal coordination : angle 1.09892 / 0.55 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 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: 13 poor density : 149 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8661 (t0) cc_final: 0.8307 (t0) REVERT: B 118 ASP cc_start: 0.8939 (t0) cc_final: 0.8611 (t0) REVERT: B 208 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8424 (mtp85) REVERT: B 257 LYS cc_start: 0.8398 (tppt) cc_final: 0.8115 (mttt) REVERT: C 30 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8336 (mtm-85) REVERT: C 110 ASP cc_start: 0.8546 (t0) cc_final: 0.8010 (t0) REVERT: D 26 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 125 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8280 (mt-10) REVERT: D 137 ASN cc_start: 0.8041 (t0) cc_final: 0.7611 (t0) REVERT: D 180 ASP cc_start: 0.8747 (t0) cc_final: 0.8376 (t0) REVERT: E 8 GLU cc_start: 0.7309 (pp20) cc_final: 0.7021 (pp20) REVERT: E 214 ILE cc_start: 0.9379 (tp) cc_final: 0.9047 (pp) outliers start: 13 outliers final: 8 residues processed: 155 average time/residue: 0.6064 time to fit residues: 98.2635 Evaluate side-chains 151 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain E residue 227 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.059704 restraints weight = 15464.484| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.07 r_work: 0.2592 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7848 Z= 0.159 Angle : 0.601 7.795 10673 Z= 0.300 Chirality : 0.040 0.157 1318 Planarity : 0.005 0.059 1313 Dihedral : 6.386 75.996 1138 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.56 % Allowed : 14.49 % Favored : 83.95 % 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: 2.31 (0.28), residues: 994 helix: 2.67 (0.22), residues: 597 sheet: 1.33 (0.58), residues: 86 loop : -0.77 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 108 TYR 0.010 0.001 TYR B 114 PHE 0.009 0.001 PHE B 57 TRP 0.006 0.001 TRP B 143 HIS 0.005 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 7832) covalent geometry : angle 0.59983 / 0.30 (10665) hydrogen bonds : bond 0.04588 / 3.06 ( 461) hydrogen bonds : angle 4.18604 / 3.05 ( 1365) metal coordination : bond 0.00867 / 0.33 ( 16) metal coordination : angle 1.55188 / 0.77 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8805 (t0) cc_final: 0.8435 (t0) REVERT: B 118 ASP cc_start: 0.9010 (t0) cc_final: 0.8533 (t0) REVERT: B 208 ARG cc_start: 0.8714 (mtp85) cc_final: 0.8495 (mtp85) REVERT: B 257 LYS cc_start: 0.8157 (tppt) cc_final: 0.7865 (mttt) REVERT: C 110 ASP cc_start: 0.8542 (t0) cc_final: 0.7810 (t0) REVERT: C 125 GLU cc_start: 0.9040 (mp0) cc_final: 0.8839 (pm20) REVERT: C 213 MET cc_start: 0.8784 (ttt) cc_final: 0.8389 (ttt) REVERT: D 8 GLU cc_start: 0.7517 (mp0) cc_final: 0.7140 (mp0) REVERT: D 26 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 75 LYS cc_start: 0.9208 (tptm) cc_final: 0.8877 (tppp) REVERT: D 125 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8333 (mt-10) REVERT: D 137 ASN cc_start: 0.8573 (t0) cc_final: 0.8110 (t0) REVERT: D 164 ASP cc_start: 0.9007 (t70) cc_final: 0.8779 (t0) REVERT: D 176 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8779 (mtp) REVERT: D 180 ASP cc_start: 0.8774 (t0) cc_final: 0.8271 (t0) REVERT: D 183 LEU cc_start: 0.9089 (mt) cc_final: 0.8812 (mm) REVERT: D 195 ASN cc_start: 0.8898 (t0) cc_final: 0.8384 (t0) REVERT: E 8 GLU cc_start: 0.7452 (pp20) cc_final: 0.6977 (pp20) REVERT: E 75 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8873 (mtpp) REVERT: E 180 ASP cc_start: 0.8882 (t70) cc_final: 0.8615 (t0) REVERT: E 187 LYS cc_start: 0.9404 (mmmt) cc_final: 0.9116 (mmmm) REVERT: E 214 ILE cc_start: 0.9344 (tp) cc_final: 0.9099 (pp) outliers start: 13 outliers final: 3 residues processed: 162 average time/residue: 0.5971 time to fit residues: 100.9508 Evaluate side-chains 145 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 227 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.063971 restraints weight = 15997.288| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.00 r_work: 0.2612 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7848 Z= 0.140 Angle : 0.589 8.069 10673 Z= 0.295 Chirality : 0.040 0.167 1318 Planarity : 0.005 0.044 1313 Dihedral : 6.343 80.653 1138 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.44 % Allowed : 14.85 % Favored : 83.71 % 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: 2.37 (0.28), residues: 994 helix: 2.72 (0.22), residues: 598 sheet: 1.36 (0.57), residues: 86 loop : -0.76 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 77 TYR 0.011 0.001 TYR C 58 PHE 0.008 0.001 PHE B 57 TRP 0.005 0.001 TRP B 143 HIS 0.003 0.001 HIS D 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7832) covalent geometry : angle 0.58851 / 0.30 (10665) hydrogen bonds : bond 0.04153 / 2.77 ( 461) hydrogen bonds : angle 4.02993 / 2.95 ( 1365) metal coordination : bond 0.00664 / 0.26 ( 16) metal coordination : angle 1.07588 / 0.53 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8865 (t0) cc_final: 0.8459 (t0) REVERT: B 118 ASP cc_start: 0.9027 (t0) cc_final: 0.8491 (t0) REVERT: B 208 ARG cc_start: 0.8718 (mtp85) cc_final: 0.8466 (mtp85) REVERT: C 3 GLU cc_start: 0.9236 (pm20) cc_final: 0.8922 (pm20) REVERT: C 4 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9234 (mt) REVERT: C 110 ASP cc_start: 0.8752 (t0) cc_final: 0.8036 (t0) REVERT: C 213 MET cc_start: 0.8801 (ttt) cc_final: 0.8364 (ttt) REVERT: D 8 GLU cc_start: 0.7648 (mp0) cc_final: 0.7184 (mp0) REVERT: D 26 GLU cc_start: 0.8156 (tm-30) cc_final: 0.6734 (tm-30) REVERT: D 28 LYS cc_start: 0.8637 (mmmm) cc_final: 0.8274 (mmpt) REVERT: D 125 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8376 (mt-10) REVERT: D 137 ASN cc_start: 0.8691 (t0) cc_final: 0.8194 (t0) REVERT: D 176 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8753 (mtp) REVERT: D 180 ASP cc_start: 0.8840 (t0) cc_final: 0.8292 (t0) REVERT: D 183 LEU cc_start: 0.9162 (mt) cc_final: 0.8858 (mm) REVERT: D 195 ASN cc_start: 0.8883 (t0) cc_final: 0.8099 (t0) REVERT: E 8 GLU cc_start: 0.7584 (pp20) cc_final: 0.7101 (pp20) REVERT: E 180 ASP cc_start: 0.8817 (t70) cc_final: 0.8475 (t0) REVERT: E 214 ILE cc_start: 0.9293 (tp) cc_final: 0.9081 (pp) outliers start: 12 outliers final: 5 residues processed: 150 average time/residue: 0.6394 time to fit residues: 100.0044 Evaluate side-chains 144 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 227 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.060064 restraints weight = 15657.150| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.12 r_work: 0.2601 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7848 Z= 0.123 Angle : 0.571 8.376 10673 Z= 0.288 Chirality : 0.039 0.162 1318 Planarity : 0.004 0.043 1313 Dihedral : 6.280 86.061 1138 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.56 % Allowed : 16.53 % Favored : 81.92 % 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: 2.46 (0.28), residues: 994 helix: 2.81 (0.22), residues: 596 sheet: 1.46 (0.57), residues: 86 loop : -0.77 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.004 0.001 TYR D 160 PHE 0.014 0.001 PHE B 57 TRP 0.004 0.001 TRP B 143 HIS 0.003 0.000 HIS E 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 7832) covalent geometry : angle 0.57054 / 0.29 (10665) hydrogen bonds : bond 0.03835 / 2.55 ( 461) hydrogen bonds : angle 3.92584 / 2.88 ( 1365) metal coordination : bond 0.00526 / 0.20 ( 16) metal coordination : angle 0.94660 / 0.45 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8945 (t0) cc_final: 0.8516 (t0) REVERT: B 118 ASP cc_start: 0.9024 (t0) cc_final: 0.8443 (t0) REVERT: B 257 LYS cc_start: 0.8275 (tppt) cc_final: 0.7945 (mttt) REVERT: C 110 ASP cc_start: 0.8829 (t0) cc_final: 0.8090 (t0) REVERT: C 213 MET cc_start: 0.8761 (ttt) cc_final: 0.8354 (ttt) REVERT: D 8 GLU cc_start: 0.7674 (mp0) cc_final: 0.6916 (mp0) REVERT: D 26 GLU cc_start: 0.8092 (tm-30) cc_final: 0.6607 (tm-30) REVERT: D 28 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8182 (mmpt) REVERT: D 125 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8395 (mt-10) REVERT: D 137 ASN cc_start: 0.8748 (t0) cc_final: 0.8403 (t0) REVERT: D 180 ASP cc_start: 0.8755 (t0) cc_final: 0.8180 (t0) REVERT: D 183 LEU cc_start: 0.9163 (mt) cc_final: 0.8854 (mm) REVERT: D 185 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8356 (mtp) REVERT: D 195 ASN cc_start: 0.8885 (t0) cc_final: 0.8095 (t0) REVERT: E 8 GLU cc_start: 0.7622 (pp20) cc_final: 0.7153 (pp20) REVERT: E 66 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8947 (mmmm) REVERT: E 180 ASP cc_start: 0.8829 (t70) cc_final: 0.8519 (t0) REVERT: E 183 LEU cc_start: 0.9241 (mm) cc_final: 0.9007 (mt) REVERT: E 190 GLU cc_start: 0.8720 (tp30) cc_final: 0.8480 (tp30) REVERT: E 227 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9143 (pp) outliers start: 13 outliers final: 5 residues processed: 150 average time/residue: 0.6275 time to fit residues: 98.1756 Evaluate side-chains 149 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain E residue 227 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.080334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.062623 restraints weight = 15922.402| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.09 r_work: 0.2590 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7848 Z= 0.141 Angle : 0.602 8.588 10673 Z= 0.302 Chirality : 0.040 0.137 1318 Planarity : 0.004 0.044 1313 Dihedral : 6.259 88.221 1138 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.44 % Allowed : 16.89 % Favored : 81.68 % 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: 2.50 (0.27), residues: 994 helix: 2.94 (0.22), residues: 583 sheet: 1.50 (0.57), residues: 86 loop : -0.80 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 108 TYR 0.011 0.001 TYR C 58 PHE 0.013 0.001 PHE B 57 TRP 0.003 0.001 TRP B 143 HIS 0.003 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 7832) covalent geometry : angle 0.60195 / 0.30 (10665) hydrogen bonds : bond 0.03950 / 2.63 ( 461) hydrogen bonds : angle 3.90779 / 2.87 ( 1365) metal coordination : bond 0.00752 / 0.30 ( 16) metal coordination : angle 1.04386 / 0.50 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8989 (t0) cc_final: 0.8528 (t0) REVERT: B 118 ASP cc_start: 0.9004 (t0) cc_final: 0.8391 (t0) REVERT: C 110 ASP cc_start: 0.8884 (t0) cc_final: 0.8127 (t0) REVERT: C 213 MET cc_start: 0.8814 (ttt) cc_final: 0.8399 (ttt) REVERT: D 8 GLU cc_start: 0.7701 (mp0) cc_final: 0.6916 (mp0) REVERT: D 26 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7325 (tm-30) REVERT: D 125 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8372 (mt-10) REVERT: D 164 ASP cc_start: 0.8960 (t70) cc_final: 0.8748 (t0) REVERT: D 180 ASP cc_start: 0.8791 (t0) cc_final: 0.8221 (t0) REVERT: D 183 LEU cc_start: 0.9235 (mt) cc_final: 0.8931 (mm) REVERT: D 195 ASN cc_start: 0.8917 (t0) cc_final: 0.8084 (t0) REVERT: E 8 GLU cc_start: 0.7657 (pp20) cc_final: 0.7198 (pp20) REVERT: E 62 LYS cc_start: 0.8514 (mtpt) cc_final: 0.7848 (tmtt) REVERT: E 66 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8958 (mmmm) REVERT: E 180 ASP cc_start: 0.8902 (t70) cc_final: 0.8570 (t0) REVERT: E 183 LEU cc_start: 0.9304 (mm) cc_final: 0.9010 (mt) REVERT: E 187 LYS cc_start: 0.9364 (mmmt) cc_final: 0.9159 (mmmm) REVERT: E 190 GLU cc_start: 0.8730 (tp30) cc_final: 0.8420 (tp30) REVERT: E 227 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9235 (pp) outliers start: 12 outliers final: 7 residues processed: 153 average time/residue: 0.7027 time to fit residues: 112.2459 Evaluate side-chains 144 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain E residue 227 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.081702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.063808 restraints weight = 15821.715| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.91 r_work: 0.2631 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7848 Z= 0.128 Angle : 0.628 9.081 10673 Z= 0.316 Chirality : 0.039 0.138 1318 Planarity : 0.005 0.045 1313 Dihedral : 6.210 86.859 1138 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.84 % Allowed : 18.80 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.27), residues: 994 helix: 2.97 (0.22), residues: 583 sheet: 1.79 (0.64), residues: 66 loop : -0.84 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 138 TYR 0.005 0.001 TYR B 58 PHE 0.014 0.001 PHE B 57 TRP 0.004 0.000 TRP B 143 HIS 0.002 0.000 HIS E 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7832) covalent geometry : angle 0.62763 / 0.32 (10665) hydrogen bonds : bond 0.03590 / 2.39 ( 461) hydrogen bonds : angle 3.80553 / 2.80 ( 1365) metal coordination : bond 0.00495 / 0.20 ( 16) metal coordination : angle 0.73181 / 0.33 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8996 (t0) cc_final: 0.8524 (t0) REVERT: B 118 ASP cc_start: 0.9088 (t0) cc_final: 0.8414 (t0) REVERT: C 110 ASP cc_start: 0.8936 (t0) cc_final: 0.8311 (t0) REVERT: C 213 MET cc_start: 0.8852 (ttt) cc_final: 0.8454 (ttt) REVERT: C 257 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7785 (mmpt) REVERT: D 8 GLU cc_start: 0.7756 (mp0) cc_final: 0.6958 (mp0) REVERT: D 26 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7258 (tm-30) REVERT: D 28 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8390 (mmmm) REVERT: D 125 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8342 (mt-10) REVERT: D 137 ASN cc_start: 0.8681 (t0) cc_final: 0.8374 (t0) REVERT: D 180 ASP cc_start: 0.8739 (t0) cc_final: 0.8167 (t0) REVERT: D 183 LEU cc_start: 0.9261 (mt) cc_final: 0.8972 (mm) REVERT: D 195 ASN cc_start: 0.8884 (t0) cc_final: 0.8523 (t0) REVERT: E 8 GLU cc_start: 0.7693 (pp20) cc_final: 0.7246 (pp20) REVERT: E 62 LYS cc_start: 0.8521 (mtpt) cc_final: 0.7954 (tmtt) REVERT: E 75 LYS cc_start: 0.9284 (mmmt) cc_final: 0.8988 (mmmm) REVERT: E 180 ASP cc_start: 0.8900 (t70) cc_final: 0.8595 (t0) REVERT: E 183 LEU cc_start: 0.9353 (mm) cc_final: 0.9055 (mt) REVERT: E 187 LYS cc_start: 0.9386 (mmmt) cc_final: 0.9168 (mmmm) REVERT: E 190 GLU cc_start: 0.8701 (tp30) cc_final: 0.8339 (tp30) outliers start: 7 outliers final: 6 residues processed: 145 average time/residue: 0.7418 time to fit residues: 112.1631 Evaluate side-chains 148 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 9.9990 chunk 11 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.079654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062120 restraints weight = 16427.513| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.07 r_work: 0.2583 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7848 Z= 0.154 Angle : 0.664 9.451 10673 Z= 0.332 Chirality : 0.040 0.142 1318 Planarity : 0.005 0.071 1313 Dihedral : 6.193 86.070 1138 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.84 % Allowed : 19.64 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.27), residues: 994 helix: 2.98 (0.22), residues: 582 sheet: 1.93 (0.64), residues: 66 loop : -0.91 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 108 TYR 0.010 0.001 TYR C 58 PHE 0.005 0.001 PHE E 213 TRP 0.004 0.001 TRP B 143 HIS 0.003 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 7832) covalent geometry : angle 0.66298 / 0.33 (10665) hydrogen bonds : bond 0.03917 / 2.62 ( 461) hydrogen bonds : angle 3.87042 / 2.85 ( 1365) metal coordination : bond 0.00932 / 0.39 ( 16) metal coordination : angle 1.21648 / 0.61 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8986 (t0) cc_final: 0.8496 (t0) REVERT: B 118 ASP cc_start: 0.9018 (t0) cc_final: 0.8315 (t0) REVERT: C 110 ASP cc_start: 0.8961 (t0) cc_final: 0.8344 (t0) REVERT: D 8 GLU cc_start: 0.7693 (mp0) cc_final: 0.6864 (mp0) REVERT: D 26 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7176 (tm-30) REVERT: D 28 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8347 (mmmm) REVERT: D 125 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8356 (mt-10) REVERT: D 137 ASN cc_start: 0.8751 (t0) cc_final: 0.8352 (t0) REVERT: D 164 ASP cc_start: 0.8958 (t70) cc_final: 0.8752 (t0) REVERT: D 180 ASP cc_start: 0.8782 (t0) cc_final: 0.8182 (t0) REVERT: D 183 LEU cc_start: 0.9288 (mt) cc_final: 0.8989 (mm) REVERT: D 195 ASN cc_start: 0.8858 (t0) cc_final: 0.8483 (t0) REVERT: E 8 GLU cc_start: 0.7701 (pp20) cc_final: 0.7220 (pp20) REVERT: E 28 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8082 (mmmm) REVERT: E 62 LYS cc_start: 0.8546 (mtpt) cc_final: 0.7924 (tmtt) REVERT: E 66 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8934 (mmmm) REVERT: E 180 ASP cc_start: 0.8902 (t70) cc_final: 0.8340 (t0) REVERT: E 183 LEU cc_start: 0.9339 (mm) cc_final: 0.8991 (mt) REVERT: E 190 GLU cc_start: 0.8749 (tp30) cc_final: 0.8391 (tp30) outliers start: 7 outliers final: 7 residues processed: 145 average time/residue: 0.7506 time to fit residues: 113.4789 Evaluate side-chains 144 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.061298 restraints weight = 16148.741| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.05 r_work: 0.2567 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7848 Z= 0.200 Angle : 0.698 13.031 10673 Z= 0.348 Chirality : 0.041 0.150 1318 Planarity : 0.005 0.056 1313 Dihedral : 6.322 88.392 1138 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.20 % Allowed : 19.64 % Favored : 79.16 % 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: 994 helix: 2.95 (0.22), residues: 581 sheet: 1.66 (0.57), residues: 86 loop : -0.83 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 108 TYR 0.008 0.001 TYR D 160 PHE 0.010 0.001 PHE D 213 TRP 0.004 0.001 TRP B 28 HIS 0.003 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 ( 7832) covalent geometry : angle 0.69684 / 0.35 (10665) hydrogen bonds : bond 0.04532 / 3.05 ( 461) hydrogen bonds : angle 4.04408 / 2.97 ( 1365) metal coordination : bond 0.01340 / 0.56 ( 16) metal coordination : angle 1.55638 / 0.74 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.8988 (t0) cc_final: 0.8499 (t0) REVERT: B 118 ASP cc_start: 0.8991 (t0) cc_final: 0.8360 (t0) REVERT: C 108 ARG cc_start: 0.8292 (tpp80) cc_final: 0.7654 (mmm160) REVERT: C 110 ASP cc_start: 0.8849 (t0) cc_final: 0.8272 (t0) REVERT: D 8 GLU cc_start: 0.7663 (mp0) cc_final: 0.6788 (mp0) REVERT: D 26 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7169 (tm-30) REVERT: D 28 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8491 (mmmm) REVERT: D 125 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8326 (mt-10) REVERT: D 137 ASN cc_start: 0.8807 (t0) cc_final: 0.8386 (t0) REVERT: D 180 ASP cc_start: 0.8902 (t0) cc_final: 0.8332 (t0) REVERT: D 183 LEU cc_start: 0.9343 (mt) cc_final: 0.9027 (mm) REVERT: D 195 ASN cc_start: 0.8865 (t0) cc_final: 0.8533 (t0) REVERT: D 213 PHE cc_start: 0.9217 (m-10) cc_final: 0.8904 (m-10) REVERT: E 8 GLU cc_start: 0.7786 (pp20) cc_final: 0.7288 (pp20) REVERT: E 28 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8120 (mmmm) REVERT: E 62 LYS cc_start: 0.8528 (mtpt) cc_final: 0.7946 (tmtt) REVERT: E 79 ASP cc_start: 0.8654 (t0) cc_final: 0.8248 (t70) REVERT: E 180 ASP cc_start: 0.9029 (t70) cc_final: 0.8536 (t0) REVERT: E 183 LEU cc_start: 0.9365 (mm) cc_final: 0.8988 (mt) REVERT: E 190 GLU cc_start: 0.8753 (tp30) cc_final: 0.8384 (tp30) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 0.7577 time to fit residues: 115.3730 Evaluate side-chains 150 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 0.0040 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.061354 restraints weight = 16157.142| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.11 r_work: 0.2648 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7848 Z= 0.136 Angle : 0.710 12.871 10673 Z= 0.350 Chirality : 0.040 0.145 1318 Planarity : 0.005 0.063 1313 Dihedral : 6.090 86.506 1136 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.72 % Allowed : 20.36 % Favored : 78.92 % 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: 2.48 (0.28), residues: 994 helix: 2.98 (0.22), residues: 582 sheet: 2.06 (0.64), residues: 66 loop : -0.91 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 108 TYR 0.011 0.001 TYR C 58 PHE 0.005 0.001 PHE C 34 TRP 0.004 0.001 TRP C 145 HIS 0.002 0.000 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7832) covalent geometry : angle 0.70946 / 0.35 (10665) hydrogen bonds : bond 0.03745 / 2.50 ( 461) hydrogen bonds : angle 3.86101 / 2.84 ( 1365) metal coordination : bond 0.00518 / 0.20 ( 16) metal coordination : angle 0.94242 / 0.45 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 110 ASP cc_start: 0.9064 (t0) cc_final: 0.8529 (t0) REVERT: B 118 ASP cc_start: 0.9033 (t0) cc_final: 0.8435 (t0) REVERT: B 257 LYS cc_start: 0.8293 (tppt) cc_final: 0.7834 (tttt) REVERT: C 108 ARG cc_start: 0.8233 (tpp80) cc_final: 0.7618 (mmm160) REVERT: C 110 ASP cc_start: 0.8824 (t0) cc_final: 0.8248 (t0) REVERT: D 8 GLU cc_start: 0.7690 (mp0) cc_final: 0.6846 (mp0) REVERT: D 26 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7183 (tm-30) REVERT: D 28 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8486 (mmmm) REVERT: D 125 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8450 (mt-10) REVERT: D 137 ASN cc_start: 0.8962 (t0) cc_final: 0.8600 (t0) REVERT: D 164 ASP cc_start: 0.9061 (t70) cc_final: 0.8840 (t0) REVERT: D 180 ASP cc_start: 0.8874 (t0) cc_final: 0.8364 (t0) REVERT: D 183 LEU cc_start: 0.9363 (mt) cc_final: 0.9110 (mm) REVERT: D 195 ASN cc_start: 0.8923 (t0) cc_final: 0.8573 (t0) REVERT: E 8 GLU cc_start: 0.7821 (pp20) cc_final: 0.7367 (pp20) REVERT: E 28 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8229 (mmmm) REVERT: E 62 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8110 (tmtt) REVERT: E 79 ASP cc_start: 0.8641 (t0) cc_final: 0.8299 (t70) REVERT: E 180 ASP cc_start: 0.8943 (t70) cc_final: 0.8509 (t0) REVERT: E 183 LEU cc_start: 0.9398 (mm) cc_final: 0.9036 (mt) REVERT: E 190 GLU cc_start: 0.8715 (tp30) cc_final: 0.8341 (tp30) outliers start: 6 outliers final: 7 residues processed: 150 average time/residue: 0.7059 time to fit residues: 110.4956 Evaluate side-chains 147 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain E residue 163 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 88 optimal weight: 0.0070 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.061934 restraints weight = 14973.542| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.12 r_work: 0.2664 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7848 Z= 0.133 Angle : 0.715 12.968 10673 Z= 0.353 Chirality : 0.039 0.143 1318 Planarity : 0.005 0.057 1313 Dihedral : 5.823 80.920 1136 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.72 % Allowed : 20.72 % Favored : 78.56 % 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: 2.55 (0.27), residues: 994 helix: 3.04 (0.22), residues: 582 sheet: 2.08 (0.65), residues: 66 loop : -0.90 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 108 TYR 0.006 0.001 TYR C 114 PHE 0.010 0.001 PHE D 213 TRP 0.004 0.000 TRP C 145 HIS 0.002 0.000 HIS E 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 7832) covalent geometry : angle 0.71465 / 0.35 (10665) hydrogen bonds : bond 0.03364 / 2.23 ( 461) hydrogen bonds : angle 3.77509 / 2.79 ( 1365) metal coordination : bond 0.00327 / 0.12 ( 16) metal coordination : angle 0.68544 / 0.31 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.85 seconds wall clock time: 41 minutes 49.64 seconds (2509.64 seconds total)