Starting phenix.real_space_refine on Wed Mar 4 05:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3s_62027/03_2026/9k3s_62027_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3s_62027/03_2026/9k3s_62027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k3s_62027/03_2026/9k3s_62027_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3s_62027/03_2026/9k3s_62027_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k3s_62027/03_2026/9k3s_62027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3s_62027/03_2026/9k3s_62027.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.098 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 7074 2.51 5 N 1805 2.21 5 O 2005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10942 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2208 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 12, 'TRANS': 275} Chain: "B" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2314 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain: "C" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1957 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "D" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1957 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "E" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2437 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.49, per 1000 atoms: 0.23 Number of scatterers: 10942 At special positions: 0 Unit cell: (76.184, 90.736, 147.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 7 15.00 Mg 2 11.99 O 2005 8.00 N 1805 7.00 C 7074 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: 0.80 Conformation dependent library (CDL) restraints added in 426.5 milliseconds 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2588 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 7 sheets defined 60.7% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 9 through 57 removed outlier: 3.548A pdb=" N ALA A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 79 through 111 Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.810A pdb=" N VAL A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.889A pdb=" N GLY A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.734A pdb=" N ARG A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.708A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.523A pdb=" N MET A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 290 removed outlier: 3.680A pdb=" N LEU A 273 " --> pdb=" O TRP A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 removed outlier: 3.664A pdb=" N ILE B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 71 through 103 Proline residue: B 91 - end of helix Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 119 through 122 removed outlier: 3.809A pdb=" N ILE B 122 " --> pdb=" O LEU B 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 151 removed outlier: 4.132A pdb=" N LEU B 138 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 169 through 194 Proline residue: B 183 - end of helix removed outlier: 3.514A pdb=" N VAL B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 207 removed outlier: 3.718A pdb=" N LYS B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 223 through 240 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 266 through 275 Processing helix chain 'B' and resid 281 through 313 removed outlier: 3.921A pdb=" N ALA B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 317 removed outlier: 3.781A pdb=" N GLY B 317 " --> pdb=" O LYS B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 317' Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.574A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.727A pdb=" N GLU C 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 62 " --> pdb=" O MET C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 removed outlier: 3.753A pdb=" N LEU C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 119 removed outlier: 3.626A pdb=" N ILE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 115 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 117 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 137 removed outlier: 3.826A pdb=" N GLU C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 169 Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.522A pdb=" N GLU C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.850A pdb=" N LEU D 62 " --> pdb=" O MET D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 106 through 119 removed outlier: 3.624A pdb=" N ILE D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 117 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.517A pdb=" N ARG D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 236 through 242 Processing helix chain 'D' and resid 245 through 253 Processing helix chain 'E' and resid 12 through 27 Processing helix chain 'E' and resid 37 through 48 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 113 through 120 removed outlier: 3.800A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 153 removed outlier: 3.563A pdb=" N LYS E 151 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 152 " --> pdb=" O TYR E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 196 through 203 Processing helix chain 'E' and resid 220 through 230 removed outlier: 3.706A pdb=" N GLY E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 284 Processing helix chain 'E' and resid 284 through 291 Processing helix chain 'E' and resid 297 through 309 removed outlier: 3.692A pdb=" N LYS E 309 " --> pdb=" O ARG E 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 23 through 34 removed outlier: 3.521A pdb=" N PHE C 23 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 18 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS C 27 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 16 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 29 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG C 14 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU C 31 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN C 12 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE C 33 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL C 13 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU C 73 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASN C 15 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU C 71 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP C 77 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 96 removed outlier: 6.777A pdb=" N GLY C 94 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASP C 178 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 96 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR C 39 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR C 222 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE C 233 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE C 224 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 23 through 34 removed outlier: 3.572A pdb=" N PHE D 23 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE D 18 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS D 27 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU D 16 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 29 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG D 14 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU D 31 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN D 12 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE D 33 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL D 13 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU D 73 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASN D 15 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU D 71 " --> pdb=" O ASN D 15 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 93 through 96 removed outlier: 6.221A pdb=" N THR D 39 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR D 226 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 35 removed outlier: 9.180A pdb=" N PHE E 52 " --> pdb=" O SER E 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR E 5 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N ALA E 54 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA E 7 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL E 75 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE E 258 " --> pdb=" O PRO E 73 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE E 260 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN E 71 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA E 131 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N TYR E 193 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL E 133 " --> pdb=" O TYR E 193 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N GLU E 195 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 12.853A pdb=" N ARG E 135 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=AA7, first strand: chain 'E' and resid 263 through 264 608 hydrogen bonds defined for protein. 1773 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: 1.67 Time building geometry restraints manager: 1.00 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: 3459 1.34 - 1.46: 2435 1.46 - 1.58: 5185 1.58 - 1.70: 10 1.70 - 1.81: 88 Bond restraints: 11177 Sorted by residual: bond pdb=" N THR A 9 " pdb=" CA THR A 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N LYS B 14 " pdb=" CA LYS B 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N GLU E 1 " pdb=" CA GLU E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" C1' ATP C 701 " pdb=" O4' ATP C 701 " ideal model delta sigma weight residual 1.416 1.399 0.017 1.30e-02 5.92e+03 1.62e+00 bond pdb=" C1' ATP D 701 " pdb=" O4' ATP D 701 " ideal model delta sigma weight residual 1.416 1.400 0.016 1.30e-02 5.92e+03 1.43e+00 ... (remaining 11172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 14892 1.36 - 2.72: 212 2.72 - 4.08: 68 4.08 - 5.45: 6 5.45 - 6.81: 7 Bond angle restraints: 15185 Sorted by residual: angle pdb=" C3' ATP D 701 " pdb=" C4' ATP D 701 " pdb=" C5' ATP D 701 " ideal model delta sigma weight residual 115.19 110.18 5.01 1.76e+00 3.23e-01 8.11e+00 angle pdb=" C3' ATP C 701 " pdb=" C4' ATP C 701 " pdb=" C5' ATP C 701 " ideal model delta sigma weight residual 115.19 110.26 4.93 1.76e+00 3.23e-01 7.84e+00 angle pdb=" C LEU A 233 " pdb=" CA LEU A 233 " pdb=" CB LEU A 233 " ideal model delta sigma weight residual 110.42 115.93 -5.51 1.99e+00 2.53e-01 7.67e+00 angle pdb=" C5' ATP D 701 " pdb=" C4' ATP D 701 " pdb=" O4' ATP D 701 " ideal model delta sigma weight residual 109.53 105.85 3.68 1.44e+00 4.84e-01 6.55e+00 angle pdb=" C5' ATP C 701 " pdb=" C4' ATP C 701 " pdb=" O4' ATP C 701 " ideal model delta sigma weight residual 109.53 105.98 3.55 1.44e+00 4.84e-01 6.10e+00 ... (remaining 15180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5993 17.78 - 35.57: 496 35.57 - 53.35: 146 53.35 - 71.14: 29 71.14 - 88.92: 8 Dihedral angle restraints: 6672 sinusoidal: 2641 harmonic: 4031 Sorted by residual: dihedral pdb=" CA ALA A 291 " pdb=" C ALA A 291 " pdb=" N LYS A 292 " pdb=" CA LYS A 292 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG D 217 " pdb=" C ARG D 217 " pdb=" N CYS D 218 " pdb=" CA CYS D 218 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLN A 164 " pdb=" C GLN A 164 " pdb=" N VAL A 165 " pdb=" CA VAL A 165 " ideal model delta harmonic sigma weight residual 180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1524 0.057 - 0.115: 193 0.115 - 0.172: 26 0.172 - 0.229: 0 0.229 - 0.287: 6 Chirality restraints: 1749 Sorted by residual: chirality pdb=" C2' ATP D 701 " pdb=" C1' ATP D 701 " pdb=" C3' ATP D 701 " pdb=" O2' ATP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C2' ATP C 701 " pdb=" C1' ATP C 701 " pdb=" C3' ATP C 701 " pdb=" O2' ATP C 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C3' ATP C 701 " pdb=" C2' ATP C 701 " pdb=" C4' ATP C 701 " pdb=" O3' ATP C 701 " both_signs ideal model delta sigma weight residual False -2.63 -2.89 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1746 not shown) Planarity restraints: 1898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 140 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C ALA B 140 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA B 140 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 141 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ILE A 198 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 198 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 199 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 64 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B 65 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 65 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 65 " 0.017 5.00e-02 4.00e+02 ... (remaining 1895 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 32 2.52 - 3.11: 7831 3.11 - 3.71: 15781 3.71 - 4.30: 22923 4.30 - 4.90: 40111 Nonbonded interactions: 86678 Sorted by model distance: nonbonded pdb=" OG SER D 50 " pdb="MG MG D 702 " model vdw 1.923 2.170 nonbonded pdb=" O LYS E 309 " pdb=" OG1 THR E 310 " model vdw 2.242 3.040 nonbonded pdb=" NZ LYS E 107 " pdb=" OE1 GLU E 155 " model vdw 2.243 3.120 nonbonded pdb=" O SER E 218 " pdb=" ND2 ASN E 223 " model vdw 2.263 3.120 nonbonded pdb=" OE1 GLN D 98 " pdb="MG MG D 702 " model vdw 2.279 2.170 ... (remaining 86673 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.002 0.033 11177 Z= 0.111 Angle : 0.492 6.808 15185 Z= 0.265 Chirality : 0.041 0.287 1749 Planarity : 0.003 0.030 1898 Dihedral : 14.917 88.920 4084 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.70 % Allowed : 11.03 % Favored : 88.27 % 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: 1.11 (0.23), residues: 1397 helix: 1.88 (0.19), residues: 785 sheet: 0.94 (0.48), residues: 116 loop : -1.23 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 123 TYR 0.009 0.001 TYR A 107 PHE 0.009 0.001 PHE A 40 TRP 0.006 0.001 TRP A 195 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00223 (11177) covalent geometry : angle 0.49212 (15185) hydrogen bonds : bond 0.16091 ( 608) hydrogen bonds : angle 5.50964 ( 1773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.436 Fit side-chains REVERT: A 123 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: A 126 ASP cc_start: 0.7952 (m-30) cc_final: 0.7572 (m-30) REVERT: B 50 GLN cc_start: 0.8123 (tp40) cc_final: 0.7784 (tp40) REVERT: B 102 GLU cc_start: 0.7765 (tp30) cc_final: 0.7287 (mp0) REVERT: B 195 GLN cc_start: 0.8676 (mm110) cc_final: 0.8416 (mp10) REVERT: C 242 LYS cc_start: 0.7414 (mttp) cc_final: 0.7122 (mtmm) REVERT: C 249 GLU cc_start: 0.8157 (tt0) cc_final: 0.7769 (tp30) REVERT: D 120 LYS cc_start: 0.8317 (tttp) cc_final: 0.7868 (mtmm) REVERT: E 112 ASP cc_start: 0.8120 (t0) cc_final: 0.6847 (p0) REVERT: E 155 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7325 (mt-10) outliers start: 8 outliers final: 7 residues processed: 126 average time/residue: 0.7323 time to fit residues: 98.1388 Evaluate side-chains 124 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.092597 restraints weight = 13162.538| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.10 r_work: 0.2863 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11177 Z= 0.143 Angle : 0.523 5.058 15185 Z= 0.278 Chirality : 0.041 0.158 1749 Planarity : 0.004 0.037 1898 Dihedral : 7.469 79.054 1572 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.48 % Allowed : 10.43 % Favored : 88.10 % 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: 1.12 (0.23), residues: 1397 helix: 1.85 (0.19), residues: 795 sheet: 0.93 (0.48), residues: 117 loop : -1.23 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 161 TYR 0.012 0.001 TYR D 20 PHE 0.013 0.001 PHE E 277 TRP 0.008 0.001 TRP B 58 HIS 0.004 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00334 (11177) covalent geometry : angle 0.52323 (15185) hydrogen bonds : bond 0.05992 ( 608) hydrogen bonds : angle 4.49296 ( 1773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: A 126 ASP cc_start: 0.8167 (m-30) cc_final: 0.7789 (m-30) REVERT: B 50 GLN cc_start: 0.7888 (tp40) cc_final: 0.7514 (tp40) REVERT: B 63 ASP cc_start: 0.8666 (t0) cc_final: 0.8148 (t70) REVERT: B 102 GLU cc_start: 0.7795 (tp30) cc_final: 0.7380 (mp0) REVERT: B 195 GLN cc_start: 0.8668 (mm110) cc_final: 0.8412 (mp10) REVERT: B 237 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8383 (tpt170) REVERT: C 249 GLU cc_start: 0.7976 (tt0) cc_final: 0.7593 (tp30) REVERT: E 112 ASP cc_start: 0.8146 (t0) cc_final: 0.6842 (p0) REVERT: E 155 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7283 (mt-10) outliers start: 17 outliers final: 4 residues processed: 132 average time/residue: 0.7733 time to fit residues: 108.4756 Evaluate side-chains 119 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 133 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.094277 restraints weight = 13342.666| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.08 r_work: 0.2925 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11177 Z= 0.119 Angle : 0.480 5.067 15185 Z= 0.254 Chirality : 0.040 0.148 1749 Planarity : 0.004 0.038 1898 Dihedral : 7.243 74.741 1563 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.65 % Allowed : 10.95 % Favored : 87.40 % 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: 1.18 (0.23), residues: 1397 helix: 1.95 (0.19), residues: 790 sheet: 0.92 (0.49), residues: 116 loop : -1.25 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.009 0.001 TYR D 20 PHE 0.012 0.001 PHE E 277 TRP 0.008 0.001 TRP B 58 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00266 (11177) covalent geometry : angle 0.48001 (15185) hydrogen bonds : bond 0.05186 ( 608) hydrogen bonds : angle 4.26223 ( 1773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.416 Fit side-chains REVERT: A 123 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: A 126 ASP cc_start: 0.8141 (m-30) cc_final: 0.7684 (m-30) REVERT: A 230 PHE cc_start: 0.8312 (m-80) cc_final: 0.8102 (m-80) REVERT: B 50 GLN cc_start: 0.7807 (tp40) cc_final: 0.7419 (tp-100) REVERT: B 102 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: B 195 GLN cc_start: 0.8701 (mm110) cc_final: 0.8437 (mp10) REVERT: B 237 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8384 (tpt170) REVERT: C 242 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7367 (mtmm) REVERT: C 249 GLU cc_start: 0.7958 (tt0) cc_final: 0.7576 (tp30) REVERT: D 250 ASP cc_start: 0.7803 (m-30) cc_final: 0.7518 (m-30) REVERT: E 112 ASP cc_start: 0.8169 (t0) cc_final: 0.6916 (p0) REVERT: E 155 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7301 (mt-10) outliers start: 19 outliers final: 6 residues processed: 133 average time/residue: 0.7191 time to fit residues: 101.7381 Evaluate side-chains 125 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 110 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 117 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095571 restraints weight = 13278.476| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.07 r_work: 0.2888 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11177 Z= 0.110 Angle : 0.465 5.083 15185 Z= 0.244 Chirality : 0.039 0.147 1749 Planarity : 0.004 0.038 1898 Dihedral : 7.124 72.655 1563 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.91 % Allowed : 11.47 % Favored : 86.62 % 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: 1.24 (0.23), residues: 1397 helix: 2.02 (0.19), residues: 787 sheet: 0.97 (0.49), residues: 116 loop : -1.25 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 220 TYR 0.008 0.001 TYR D 20 PHE 0.011 0.001 PHE E 277 TRP 0.008 0.001 TRP B 58 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00240 (11177) covalent geometry : angle 0.46453 (15185) hydrogen bonds : bond 0.04776 ( 608) hydrogen bonds : angle 4.12498 ( 1773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.433 Fit side-chains REVERT: A 123 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: A 126 ASP cc_start: 0.8069 (m-30) cc_final: 0.7605 (m-30) REVERT: A 230 PHE cc_start: 0.8245 (m-80) cc_final: 0.8030 (m-80) REVERT: B 50 GLN cc_start: 0.7789 (tp40) cc_final: 0.7315 (tp40) REVERT: B 102 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 195 GLN cc_start: 0.8659 (mm110) cc_final: 0.8388 (mp10) REVERT: B 237 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8259 (tpt170) REVERT: B 254 GLN cc_start: 0.8203 (mt0) cc_final: 0.7851 (mp10) REVERT: C 249 GLU cc_start: 0.7894 (tt0) cc_final: 0.7508 (tp30) REVERT: D 250 ASP cc_start: 0.7759 (m-30) cc_final: 0.7476 (m-30) REVERT: E 112 ASP cc_start: 0.8162 (t0) cc_final: 0.6913 (p0) REVERT: E 155 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7323 (mt-10) outliers start: 22 outliers final: 7 residues processed: 141 average time/residue: 0.7222 time to fit residues: 108.5986 Evaluate side-chains 128 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094420 restraints weight = 13235.404| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.12 r_work: 0.2897 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11177 Z= 0.116 Angle : 0.478 5.540 15185 Z= 0.251 Chirality : 0.039 0.143 1749 Planarity : 0.004 0.037 1898 Dihedral : 7.130 73.482 1563 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.00 % Allowed : 12.25 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1397 helix: 2.03 (0.19), residues: 787 sheet: 0.97 (0.49), residues: 116 loop : -1.27 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 220 TYR 0.009 0.001 TYR D 20 PHE 0.012 0.001 PHE E 277 TRP 0.008 0.001 TRP B 58 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00259 (11177) covalent geometry : angle 0.47768 (15185) hydrogen bonds : bond 0.04939 ( 608) hydrogen bonds : angle 4.09480 ( 1773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.332 Fit side-chains REVERT: A 123 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: A 126 ASP cc_start: 0.8035 (m-30) cc_final: 0.7634 (m-30) REVERT: B 50 GLN cc_start: 0.7774 (tp40) cc_final: 0.7388 (tp-100) REVERT: B 63 ASP cc_start: 0.8624 (t0) cc_final: 0.8153 (t70) REVERT: B 102 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: B 195 GLN cc_start: 0.8659 (mm110) cc_final: 0.8433 (mm-40) REVERT: B 237 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8307 (tpt170) REVERT: B 254 GLN cc_start: 0.8282 (mt0) cc_final: 0.7914 (mp10) REVERT: C 249 GLU cc_start: 0.7903 (tt0) cc_final: 0.7523 (tp30) REVERT: D 250 ASP cc_start: 0.7747 (m-30) cc_final: 0.7462 (m-30) REVERT: E 112 ASP cc_start: 0.8228 (t0) cc_final: 0.6953 (p0) REVERT: E 155 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7267 (mt-10) outliers start: 23 outliers final: 11 residues processed: 135 average time/residue: 0.6768 time to fit residues: 97.6146 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 252 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.094166 restraints weight = 13276.003| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.12 r_work: 0.2885 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11177 Z= 0.122 Angle : 0.482 5.308 15185 Z= 0.253 Chirality : 0.040 0.141 1749 Planarity : 0.004 0.038 1898 Dihedral : 7.181 74.913 1563 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.82 % Allowed : 12.42 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1397 helix: 2.04 (0.19), residues: 787 sheet: 0.94 (0.49), residues: 116 loop : -1.29 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 166 TYR 0.009 0.001 TYR D 20 PHE 0.012 0.001 PHE E 277 TRP 0.008 0.001 TRP B 58 HIS 0.004 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00278 (11177) covalent geometry : angle 0.48199 (15185) hydrogen bonds : bond 0.05092 ( 608) hydrogen bonds : angle 4.08825 ( 1773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.386 Fit side-chains REVERT: A 123 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: A 126 ASP cc_start: 0.8022 (m-30) cc_final: 0.7662 (m-30) REVERT: B 50 GLN cc_start: 0.7777 (tp40) cc_final: 0.7377 (tp-100) REVERT: B 102 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 195 GLN cc_start: 0.8655 (mm110) cc_final: 0.8437 (mm-40) REVERT: B 237 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8329 (tpt170) REVERT: B 254 GLN cc_start: 0.8311 (mt0) cc_final: 0.7946 (mp10) REVERT: C 249 GLU cc_start: 0.7908 (tt0) cc_final: 0.7540 (tp30) REVERT: D 61 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8214 (mm-30) REVERT: D 250 ASP cc_start: 0.7723 (m-30) cc_final: 0.7433 (m-30) REVERT: E 112 ASP cc_start: 0.8254 (t0) cc_final: 0.6976 (p0) REVERT: E 155 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7245 (mt-10) outliers start: 21 outliers final: 11 residues processed: 133 average time/residue: 0.7104 time to fit residues: 100.6522 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 128 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.094908 restraints weight = 13208.493| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.05 r_work: 0.2895 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11177 Z= 0.110 Angle : 0.469 6.627 15185 Z= 0.245 Chirality : 0.039 0.141 1749 Planarity : 0.004 0.037 1898 Dihedral : 7.082 73.016 1563 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.65 % Allowed : 12.77 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.23), residues: 1397 helix: 2.11 (0.19), residues: 787 sheet: 0.99 (0.50), residues: 116 loop : -1.26 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.008 0.001 TYR D 108 PHE 0.011 0.001 PHE E 277 TRP 0.008 0.001 TRP B 58 HIS 0.003 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00240 (11177) covalent geometry : angle 0.46907 (15185) hydrogen bonds : bond 0.04695 ( 608) hydrogen bonds : angle 4.03467 ( 1773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.464 Fit side-chains REVERT: A 123 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: A 126 ASP cc_start: 0.7984 (m-30) cc_final: 0.7636 (m-30) REVERT: B 50 GLN cc_start: 0.7754 (tp40) cc_final: 0.7379 (tp40) REVERT: B 102 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 195 GLN cc_start: 0.8688 (mm110) cc_final: 0.8472 (mm-40) REVERT: B 237 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8315 (tpt170) REVERT: C 249 GLU cc_start: 0.7900 (tt0) cc_final: 0.7551 (tp30) REVERT: D 61 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 250 ASP cc_start: 0.7747 (m-30) cc_final: 0.7463 (m-30) REVERT: E 112 ASP cc_start: 0.8247 (t0) cc_final: 0.6972 (p0) REVERT: E 155 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7268 (mt-10) outliers start: 19 outliers final: 11 residues processed: 134 average time/residue: 0.7470 time to fit residues: 106.6682 Evaluate side-chains 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 114 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN D 24 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.093496 restraints weight = 13250.588| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.09 r_work: 0.2908 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11177 Z= 0.122 Angle : 0.484 6.590 15185 Z= 0.252 Chirality : 0.040 0.140 1749 Planarity : 0.004 0.038 1898 Dihedral : 7.146 74.817 1563 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.65 % Allowed : 13.21 % Favored : 85.14 % 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: 1.27 (0.23), residues: 1397 helix: 2.06 (0.19), residues: 787 sheet: 0.98 (0.49), residues: 116 loop : -1.28 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 123 TYR 0.008 0.001 TYR D 108 PHE 0.012 0.001 PHE E 277 TRP 0.007 0.001 TRP B 58 HIS 0.004 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00277 (11177) covalent geometry : angle 0.48388 (15185) hydrogen bonds : bond 0.05052 ( 608) hydrogen bonds : angle 4.06458 ( 1773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.314 Fit side-chains REVERT: A 123 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: A 126 ASP cc_start: 0.7919 (m-30) cc_final: 0.7586 (m-30) REVERT: B 50 GLN cc_start: 0.7730 (tp40) cc_final: 0.7340 (tp40) REVERT: B 63 ASP cc_start: 0.8630 (t0) cc_final: 0.8248 (t70) REVERT: B 102 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: B 195 GLN cc_start: 0.8664 (mm110) cc_final: 0.8447 (mm-40) REVERT: B 237 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8386 (tpt170) REVERT: B 254 GLN cc_start: 0.8355 (mt0) cc_final: 0.7980 (mp10) REVERT: C 249 GLU cc_start: 0.7890 (tt0) cc_final: 0.7537 (tp30) REVERT: D 61 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 250 ASP cc_start: 0.7723 (m-30) cc_final: 0.7424 (m-30) REVERT: E 112 ASP cc_start: 0.8242 (t0) cc_final: 0.6962 (p0) REVERT: E 155 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7257 (mt-10) outliers start: 19 outliers final: 12 residues processed: 130 average time/residue: 0.6929 time to fit residues: 95.9536 Evaluate side-chains 129 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 0.0570 chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 0.0050 chunk 133 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.097520 restraints weight = 13158.114| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.05 r_work: 0.2946 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11177 Z= 0.092 Angle : 0.442 5.617 15185 Z= 0.230 Chirality : 0.038 0.141 1749 Planarity : 0.003 0.037 1898 Dihedral : 6.828 68.982 1563 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.48 % Allowed : 13.55 % Favored : 84.97 % 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: 1.48 (0.23), residues: 1397 helix: 2.23 (0.19), residues: 787 sheet: 1.10 (0.50), residues: 116 loop : -1.18 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 123 TYR 0.006 0.001 TYR D 108 PHE 0.009 0.001 PHE A 40 TRP 0.007 0.001 TRP B 58 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00185 (11177) covalent geometry : angle 0.44232 (15185) hydrogen bonds : bond 0.03911 ( 608) hydrogen bonds : angle 3.92733 ( 1773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.459 Fit side-chains REVERT: A 123 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: A 126 ASP cc_start: 0.7900 (m-30) cc_final: 0.7567 (m-30) REVERT: B 50 GLN cc_start: 0.7652 (tp40) cc_final: 0.7195 (tp40) REVERT: B 63 ASP cc_start: 0.8628 (t0) cc_final: 0.8168 (t70) REVERT: B 102 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 195 GLN cc_start: 0.8670 (mm110) cc_final: 0.8443 (mm-40) REVERT: B 237 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8273 (tpt170) REVERT: B 254 GLN cc_start: 0.8323 (mt0) cc_final: 0.7947 (mp10) REVERT: C 238 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: C 249 GLU cc_start: 0.7851 (tt0) cc_final: 0.7501 (tp30) REVERT: D 61 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8211 (mm-30) REVERT: D 250 ASP cc_start: 0.7766 (m-30) cc_final: 0.7503 (m-30) REVERT: E 112 ASP cc_start: 0.8219 (t0) cc_final: 0.6949 (p0) REVERT: E 155 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7265 (mt-10) outliers start: 17 outliers final: 7 residues processed: 137 average time/residue: 0.7093 time to fit residues: 103.7656 Evaluate side-chains 130 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 252 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095218 restraints weight = 13180.575| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.12 r_work: 0.2917 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11177 Z= 0.111 Angle : 0.473 6.441 15185 Z= 0.246 Chirality : 0.039 0.137 1749 Planarity : 0.004 0.037 1898 Dihedral : 6.882 73.289 1562 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.48 % Allowed : 13.38 % Favored : 85.14 % 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: 1.44 (0.23), residues: 1397 helix: 2.20 (0.19), residues: 787 sheet: 1.09 (0.50), residues: 116 loop : -1.20 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 123 TYR 0.008 0.001 TYR D 108 PHE 0.012 0.001 PHE E 277 TRP 0.007 0.001 TRP B 58 HIS 0.004 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00245 (11177) covalent geometry : angle 0.47269 (15185) hydrogen bonds : bond 0.04616 ( 608) hydrogen bonds : angle 3.98785 ( 1773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.424 Fit side-chains REVERT: A 123 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: A 126 ASP cc_start: 0.7978 (m-30) cc_final: 0.7627 (m-30) REVERT: B 50 GLN cc_start: 0.7724 (tp40) cc_final: 0.7315 (tp40) REVERT: B 63 ASP cc_start: 0.8657 (t0) cc_final: 0.8241 (t70) REVERT: B 102 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: B 195 GLN cc_start: 0.8657 (mm110) cc_final: 0.8424 (mm-40) REVERT: B 237 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8314 (tpt170) REVERT: C 249 GLU cc_start: 0.7870 (tt0) cc_final: 0.7522 (tp30) REVERT: D 61 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8214 (mm-30) REVERT: D 250 ASP cc_start: 0.7752 (m-30) cc_final: 0.7488 (m-30) REVERT: E 112 ASP cc_start: 0.8239 (t0) cc_final: 0.6956 (p0) REVERT: E 155 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7257 (mt-10) outliers start: 17 outliers final: 9 residues processed: 135 average time/residue: 0.7449 time to fit residues: 107.2380 Evaluate side-chains 131 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.093751 restraints weight = 13276.952| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.06 r_work: 0.2880 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11177 Z= 0.129 Angle : 0.501 6.104 15185 Z= 0.261 Chirality : 0.040 0.139 1749 Planarity : 0.004 0.039 1898 Dihedral : 7.094 76.343 1562 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 13.55 % Favored : 84.80 % 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: 1.34 (0.23), residues: 1397 helix: 2.11 (0.19), residues: 787 sheet: 1.09 (0.50), residues: 116 loop : -1.23 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 17 TYR 0.009 0.001 TYR D 108 PHE 0.013 0.001 PHE E 277 TRP 0.008 0.001 TRP B 58 HIS 0.005 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00298 (11177) covalent geometry : angle 0.50094 (15185) hydrogen bonds : bond 0.05165 ( 608) hydrogen bonds : angle 4.06476 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.01 seconds wall clock time: 59 minutes 28.88 seconds (3568.88 seconds total)